[Freesurfer] LGi computation on computer cluster
Hio We want to compute the LGI index, using our local computing cluster. the cluster does not have matlab or it's image processing toolbox on the computing nodes. Which matlab .m files does the LGI computation use? Thanks -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] LGI radius
Hi freesurfer experts is it possbile to change the radius for the LGI computation. ( it's normally set at 25 mm) we waned to try computing the LGI with a smaller radius. I looked the in the "compute_lgi.m" file, and it does not use radius, (even though radius is an input parameter for it) Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] LGI radius
HI Marie, What is the minimum radius that you would suggest to use, and still produce reliable results JOn - Original Message - From: "Marie Schaer" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, October 11, 2013 9:04:27 PM Subject: Re: [Freesurfer] LGI radius Hi Jon, The fastest way is probably to change the radius value on row 40 in mris_compute_lgi. We originally intended to make an option for setting the radius, but I realize that we forgot it in the end. I'll see if we can change it for the next version, but in the mean time change the value directly in mris_compute_lgi and you'll be fine. Best, Marie On Oct 11, 2013, at 11:02 AM, Jon Wieser wrote: > Hi freesurfer experts > is it possbile to change the radius for the LGI computation. ( it's normally > set at 25 mm) we waned to try computing the LGI with a smaller radius. > I looked the in the "compute_lgi.m" file, and it does not use radius, (even > though radius is an input parameter for it) > Thanks > Jon > > -- > Jon Wieser > Research Specialist > UW-Milwaukee > Psychology Department, Pearse Hall Rm 366 > 2441 East Hartford Ave > Milwaukee, WI 53211 > Phone: 414-229-7145 > Fax: 414-229-5219 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Pial surface interhemispheric overlap
HI bruce thanks for the info the aseg was ok, except that the Right and Left cerebral cortex lables were in adjacent voxel in the region. I modified aseg.mgz so that they didn't touch. by eraseing some of the segmentation in the space between the hemispheres. At which stage do I restart the recon-all? I think I should restart at -normalization2, since that that,s the next step after the aseg.mgz is created JOn - Original Message - From: "Bruce Fischl" To: "Jon Wieser" Cc: "freesurfer" Sent: Monday, October 21, 2013 12:46:09 PM Subject: Re: [Freesurfer] Pial surface interhemispheric overlap Hi Jon that's pretty bad. Is the aseg also incorrect there? If so, try correcting it and rerunning cheers Bruce On Mon, 21 Oct 2013, Jon Wieser wrote: > > > > Hi Freesurfer experts > I recently created surfaces with recon-all, and found that in the straight > gyrus in the medial inferior frontal lobe, the pial surfaces are overlaping > between the hemispheres. I have attached a picture to show the problem. > You can see from the picture that the pial surface from the Right hemisphere > (in Blue) and the pial surface from the left hemisphere ( in Red) are > overlapping (crossing over) to the other hemisphere.how can I fix this? > Thanks > Jon > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tracula Error
Hi anastasia, I work with Emily. the wild card she used i*.MRDC.1 specifies only the first dicom image. the dicoms are in the format: i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 i727092.MRDC.37 i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 i727128.MRDC.73 i727137.MRDC.82 i727146.MRDC.91 i727057.MRDC.2 i727066.MRDC.11 i727075.MRDC.20 i727084.MRDC.29 i727093.MRDC.38 i727102.MRDC.47 i727111.MRDC.56 i727120.MRDC.65 i727129.MRDC.74 i727138.MRDC.83 i727147.MRDC.92 i727058.MRDC.3 i727067.MRDC.12 i727076.MRDC.21 i727085.MRDC.30 i727094.MRDC.39 i727103.MRDC.48 i727112.MRDC.57 i727121.MRDC.66 i727130.MRDC.75 i727139.MRDC.84 i727148.MRDC.93 i727059.MRDC.4 i727068.MRDC.13 i727077.MRDC.22 i727086.MRDC.31 i727095.MRDC.40 i727104.MRDC.49 i727113.MRDC.58 i727122.MRDC.67 i727131.MRDC.76 i727140.MRDC.85 i727149.MRDC.94 i727060.MRDC.5 i727069.MRDC.14 i727078.MRDC.23 i727087.MRDC.32 i727096.MRDC.41 i727105.MRDC.50 i727114.MRDC.59 i727123.MRDC.68 i727132.MRDC.77 i727141.MRDC.86 i727150.MRDC.95 i727061.MRDC.6 i727070.MRDC.15 i727079.MRDC.24 i727088.MRDC.33 i727097.MRDC.42 i727106.MRDC.51 i727115.MRDC.60 i727124.MRDC.69 i727133.MRDC.78 i727142.MRDC.87 i727151.MRDC.96 i727062.MRDC.7 i727071.MRDC.16 i727080.MRDC.25 i727089.MRDC.34 i727098.MRDC.43 i727107.MRDC.52 i727116.MRDC.61 i727125.MRDC.70 i727134.MRDC.79 i727143.MRDC.88 i727152.MRDC.97 i727063.MRDC.8 i727072.MRDC.17 i727081.MRDC.26 i727090.MRDC.35 i727099.MRDC.44 i727108.MRDC.53 i727117.MRDC.62 i727126.MRDC.71 i727135.MRDC.80 i727144.MRDC.89 i727153.MRDC.98 i727064.MRDC.9 i727073.MRDC.18 i727082.MRDC.27 i727091.MRDC.36 i727100.MRDC.45 i727109.MRDC.54 i727118.MRDC.63 i727127.MRDC.72 i727136.MRDC.81 i727145.MRDC.90 i727154.MRDC.99 etc so i*.MRDC.1 would specify only the file i727056.MRDC.1, the first dicom image Jon - Original Message - From: "Anastasia Yendiki" To: ebell...@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 22, 2013 10:09:13 AM Subject: Re: [Freesurfer] Tracula Error Hi Emily - You're using "*" to specify all the dicom files in the series. You should specify just one file. BTW, do you have the latest version of freesurfer and the tutorials? This dmrirc looks like it might have been adapted from an older version of the tutorials. If so, I highly recommend downloading the latest version of everything. Hope this helps, a.y On Mon, 21 Oct 2013, ebell...@uwm.edu wrote: > Hello, > > I am running into the following error when I try to run trac-all: > > set: No match. > ERROR: must specify as many DWI dicoms as subjects > > I have taken my script and examined it line by line and have made several > attempts at debugging it. > > I was wondering if you had any suggestions? Attached is my > dmrirc_single_subject configuration. > > I am brand new to freesurfer and tracula and would appreciate any guidance > you can give me! > > Thanks! > > Emily > > - Original Message - > From: "Anastasia Yendiki" > To: ebell...@uwm.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, October 10, 2013 3:53:29 PM > Subject: Re: [Freesurfer] Tracula > > > Hi Emily - The first version of tracula was in freesurfer 5.1. However, I > would *highly* recommend using the newer version of tracula, now in 5.3, > as it has improvements in both performance and speed. > > The processing in trac-all is supposed to happen in parallel for each of > the subjects included in the configuration file, if you run trac-all on a > cluster. However, not all clusters have the same set-up, and you may have > to make modifications for it to work on your cluster, with the help of > your cluster admins. There should be previous questions on this in this > list's email archives. Let me know if you have any other questions. > > a.y > > On Thu, 10 Oct 2013, ebell...@uwm.edu wrote: > >> >> >> - Original Message - >> From: ebell...@uwm.edu >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Thursday, October 10, 2013 3:14:06 PM >> Subject: Tracula >> >> Hello, >> >> I had a question regarding batch processing in trac all. >> >> When you batch process and put in multiple subjects in your subject list in >> your configuration file, are the subjects run parallel or serial? >> >> Also, I am having a hard time finding the linux version of tracula that is >> compatible with Freesurfer version 5.0 (assuming it exists)? >> >> Thank you so much and I appreciate your guidance as I am brand new to >> freesurfer and tracula. >> >> Emily >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If
Re: [Freesurfer] Tracula Error
according to the tracula wiki: http://freesurfer.net/fswiki/FsTutorial/Tracula the program should look in the directory specified by "dcmroot" to look for the dicom list excerpt from the wiki page: Step 5: Specify the location of diffusion DICOM files set dcmroot = $TUTORIAL_DATA/diffusion_tutorial Use this variable to specify the directory under which the diffusion DICOM files for all subjects can be found. Step 6: Specify the list of input DWIs set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \ elmo.2008/orig/97000-17-01.dcm \ elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 ) Jon - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Cc: "freesurfer" , "ebelleau" Sent: Tuesday, October 22, 2013 12:24:22 PM Subject: Re: [Freesurfer] Tracula Error The problem is that the command "set dcmlist = (i*.MRDC.1)" is executed as soon as it is read. So this will end up with an empty dcmlist, because there are no files named i*.MRDC.1 in the current directory. On Tue, 22 Oct 2013, Jon Wieser wrote: > > Hi anastasia, > I work with Emily. the wild card she used i*.MRDC.1 specifies only the > first dicom image. the dicoms are in the format: > > i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 > i727092.MRDC.37 i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 > i727128.MRDC.73 i727137.MRDC.82 i727146.MRDC.91 > i727057.MRDC.2 i727066.MRDC.11 i727075.MRDC.20 i727084.MRDC.29 > i727093.MRDC.38 i727102.MRDC.47 i727111.MRDC.56 i727120.MRDC.65 > i727129.MRDC.74 i727138.MRDC.83 i727147.MRDC.92 > i727058.MRDC.3 i727067.MRDC.12 i727076.MRDC.21 i727085.MRDC.30 > i727094.MRDC.39 i727103.MRDC.48 i727112.MRDC.57 i727121.MRDC.66 > i727130.MRDC.75 i727139.MRDC.84 i727148.MRDC.93 > i727059.MRDC.4 i727068.MRDC.13 i727077.MRDC.22 i727086.MRDC.31 > i727095.MRDC.40 i727104.MRDC.49 i727113.MRDC.58 i727122.MRDC.67 > i727131.MRDC.76 i727140.MRDC.85 i727149.MRDC.94 > i727060.MRDC.5 i727069.MRDC.14 i727078.MRDC.23 i727087.MRDC.32 > i727096.MRDC.41 i727105.MRDC.50 i727114.MRDC.59 i727123.MRDC.68 > i727132.MRDC.77 i727141.MRDC.86 i727150.MRDC.95 > i727061.MRDC.6 i727070.MRDC.15 i727079.MRDC.24 i727088.MRDC.33 > i727097.MRDC.42 i727106.MRDC.51 i727115.MRDC.60 i727124.MRDC.69 > i727133.MRDC.78 i727142.MRDC.87 i727151.MRDC.96 > i727062.MRDC.7 i727071.MRDC.16 i727080.MRDC.25 i727089.MRDC.34 > i727098.MRDC.43 i727107.MRDC.52 i727116.MRDC.61 i727125.MRDC.70 > i727134.MRDC.79 i727143.MRDC.88 i727152.MRDC.97 > i727063.MRDC.8 i727072.MRDC.17 i727081.MRDC.26 i727090.MRDC.35 > i727099.MRDC.44 i727108.MRDC.53 i727117.MRDC.62 i727126.MRDC.71 > i727135.MRDC.80 i727144.MRDC.89 i727153.MRDC.98 > i727064.MRDC.9 i727073.MRDC.18 i727082.MRDC.27 i727091.MRDC.36 > i727100.MRDC.45 i727109.MRDC.54 i727118.MRDC.63 i727127.MRDC.72 > i727136.MRDC.81 i727145.MRDC.90 i727154.MRDC.99 etc > > > > so i*.MRDC.1 would specify only the file i727056.MRDC.1, the first dicom > image > > Jon > > - Original Message - > From: "Anastasia Yendiki" > To: ebell...@uwm.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, October 22, 2013 10:09:13 AM > Subject: Re: [Freesurfer] Tracula Error > > > Hi Emily - You're using "*" to specify all the dicom files in the series. > You should specify just one file. > > BTW, do you have the latest version of freesurfer and the tutorials? This > dmrirc looks like it might have been adapted from an older version of the > tutorials. If so, I highly recommend downloading the latest version of > everything. > > Hope this helps, > a.y > > On Mon, 21 Oct 2013, ebell...@uwm.edu wrote: > >> Hello, >> >> I am running into the following error when I try to run trac-all: >> >> set: No match. >> ERROR: must specify as many DWI dicoms as subjects >> >> I have taken my script and examined it line by line and have made several >> attempts at debugging it. >> >> I was wondering if you had any suggestions? Attached is my >> dmrirc_single_subject configuration. >> >> I am brand new to freesurfer and tracula and would appreciate any guidance >> you can give me! >> >> Thanks! >> >> Emily >> >> - Original Message - >> From: "Anastasia Yendiki" >> To: ebell...@uwm.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Thursday, October 10, 2013 3:53:29 PM >> Subject: Re: [Freesurfer] Tracula >> >> >> Hi Emily - The first version of tracula was in freesurfer 5.1. However, I >> would *highly* recommend using the newer version of tracula, no
Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
we install freesurfer 5.3 when we run trac-all -prep -c dmrirc the process ends with the error: tkreg2FSL: mov det = -64, ref det = 1 INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. Tue Dec 3 13:32:26 CST 2013 /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data flirt.fsl -ref /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/refvol.fslregister.nii -in /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/reg.init.dat.fsl.mat0 flirt.fsl: Command not found. ERROR: flirt Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Tue Dec 3 13:32:26 CST 2013 flirt.fsl is not in the $FREESURFER_HOME/bin directory Jon - Original Message - From: "Anastasia Yendiki" To: "Skyler Gabriel Shollenbarger" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed. You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok? a.y On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote: > Hi Anastasia, > > We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. > Is there anything to do about poor registration? > > Thank you for the fast reply. Truly appreciated. > Skyler > > - Original Message - > From: "Anastasia Yendiki" > To: "Skyler Gabriel Shollenbarger" > Cc: Freesurfer@nmr.mgh.harvard.edu > Sent: Monday, December 2, 2013 4:27:37 PM > Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts > > > Hi Skyler - Are you using freesurfer 5.1 or 5.3? > > Most likely this issue is due to poor registration, either from the > individual DWI to the individual T1, or from the individual T1 to the > template space. Or it could be that there is a problem with the > aparc+aseg. > > a.y > > On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote: > >> Hi all, >> >> I've been running DTI using tracula (fs version 5) for over 1 week on 2 >> subjects. It appears that it is having difficulty finding satisfactory >> control point fit and has attempted over 1600 tries. Any help is greatly >> appreciated. >> See error below: >> >> INFO: Distances between consecutive points are 25 24 25 26 >> WARN: Could not find satisfactory control point fit - try 1665 >> Finding center streamline >> INFO: Step is 4 voxels >> WARN: Turning off FA check for center streamline >> INFO: Step is 4 voxels >> WARN: Turning off deviation check for center streamline >> INFO: Step is 4 voxels >> INFO: Length of center streamline is 96 voxels >> Selecting 5 points on center streamline >> INFO: Step is 4 voxels >> WARN: Defaulting to equidistant control points >> INFO: Selected control points are >> 108 193 84 >> 112 173 72 >> 98 153 75 >> 74 157 75 >> 74 184 86 >> INFO: Distances between consecutive points are 24 25 24 29 >> WARN: Could not find satisfactory control point fit - try 1666 >> Finding center streamline >> INFO: Step is 4 voxels >> WARN: Turning off FA check for center streamline >> INFO: Step is 4 voxels >> WARN: Turning off deviation check for center streamline >> INFO: Step is 4 voxels >> >> >> Best, >> Skyler >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceli
Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
hi zeke, thanks for the help in the log file, if you look at the last new invocation of trac-all, it indicates that it a runing the freesurefer 5.3 version Excerpt from Log file: New invocation of trac-all Wed Dec 4 12:02:28 CST 2013 /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data /Applications/Freesurfer5.3/bin/trac-all -prep -c dmrirc_single_subject Subject freesurfer SUBJECTS_DIR /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data FREESURFER_HOME /Applications/Freesurfer5.3 Actual FREESURFER_HOME /Applications/Freesurfer5.3 - Original Message - From: "Z K" To: "Skyler Gabriel Shollenbarger" Cc: "Anastasia Yendiki" , freesurfer@nmr.mgh.harvard.edu, "Jon Wieser" Sent: Wednesday, December 4, 2013 2:29:43 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts According to the log file you sent, you are running freesurfer 5.1, leopard version. And now that I am looking at your previous email, it seems you were running the freesurfer 5.1 leopard version in that case too. It also looks like you are indeed running a 32bit snow leopard machine so please move (or completely erase) any previously installed version of freesurfer you have on your machine and download and install this one. -Zeke On 12/04/2013 03:21 PM, Skyler Gabriel Shollenbarger wrote: > Hi Zeke, > > Thanks for the help. We installed the 64bit version and got the same error. > > INFO: Distances between consecutive points in test subject's space are 5 5 6 5 > Writing output files to > /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* > dmri_train(65940) malloc: *** mmap(size=159744) failed (error code=12) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice > > Cannot allocate memory > > I've attached the error log for trac-all in case you need. > > Thanks again! > Skyler and Jon > > > - Original Message - > From: "Z K" > To: "Skyler Gabriel Shollenbarger" > Cc: "Anastasia Yendiki" , > freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, December 4, 2013 9:46:37 AM > Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts > > It looks like your running 32bit freesurfer on a 64bit machine with snow > leopard installed on it. In this case You will have to install the 64bit > version of freesurfer instead of the 32bit version you installed previously. > > You can get the version you need from the following link: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg > > Sorry for the confusion. > > -Zeke > > On 12/04/2013 10:34 AM, Skyler Gabriel Shollenbarger wrote: >> Hi Anastasia, >> >> Thanks for your help. We updated to version 5.3 and received this error: >> INFO: Distances between consecutive points in test subject's space are 5 5 6 >> 5 >> Writing output files to >> /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* >> dmri_train(44276) malloc: *** mmap(size=159744) failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice >> >> Cannot allocate memory >> >> We use Mac OS X 10.6.8 Snowleopard. >> >> Best, >> Skyler >> >> - Original Message - >> From: "Anastasia Yendiki" >> To: "Skyler Gabriel Shollenbarger" >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, December 3, 2013 1:19:55 AM >> Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts >> >> >> Hi Skyler - I would *highly* recommend using the version of tracula in >> 5.3, as there have been improvements in both performance and speed. >> >> You can check the DWI to anatomical registration by overlaying the >> aparc+aseg from the dlabel/diff directory (which is in diffusion space) on >> the FA map. Does that look ok? >> >> a.y >> >> On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote: >> >>> Hi Anastasia, >>> >>> We're using 5.1. It's likely poor registration. The aparc+aseg. looked >>> fine. Is there anything to do about poor registration? >>> >>> Thank you for the fast reply. Truly appreciated. >>> Skyler >>> >>> - Original Message - >>> From: "Anastasia Yen
Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Zeke, thanks for the info. we had installed the 64 bit lion version of freesurfer. perhaps the trac-all was engaged from the wrong (older) directory. I am nuking the old versions. and will try it again Jon - Original Message - From: "Z K" To: "Jon Wieser" Cc: "Skyler Gabriel Shollenbarger" , "freesurfer" Sent: Wednesday, December 4, 2013 5:15:47 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts Yes, you are correct. I sometimes forget these log files keep appending. But when I look at the last call of trac-all it says "freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0" which is the 32bit OSX build of FreeSurfer. The 64bit version is called ""freesurfer-Darwin-lion-stable-pub-v5.3.0" and I dont see that referenced anywhere in the log file. So it looks like that solution was never actually attempted. Im not 100% convinced this will solve your problem, but the error you are getting is almost always solved by using the 64bit version, so please download and install the 64bit version from the link I provided earlier: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg Hopefully that takes care of it. Make sure that "freesurfer-Darwin-lion-stable-pub-v5.3.0" is referenced in the log file. If you still get the error please contact us again and we'll go from there. -Zeke On 12/04/2013 05:55 PM, Jon Wieser wrote: > hi zeke, > > thanks for the help > in the log file, if you look at the last new invocation of trac-all, it > indicates that it a runing the freesurefer 5.3 version > > Excerpt from Log file: > > New invocation of trac-all > > > Wed Dec 4 12:02:28 CST 2013 > /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data > /Applications/Freesurfer5.3/bin/trac-all > -prep -c dmrirc_single_subject > Subject freesurfer > SUBJECTS_DIR > /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1064/data > FREESURFER_HOME /Applications/Freesurfer5.3 > Actual FREESURFER_HOME /Applications/Freesurfer5.3 > > > > > > - Original Message - > From: "Z K" > To: "Skyler Gabriel Shollenbarger" > Cc: "Anastasia Yendiki" , > freesurfer@nmr.mgh.harvard.edu, "Jon Wieser" > Sent: Wednesday, December 4, 2013 2:29:43 PM > Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts > > According to the log file you sent, you are running freesurfer 5.1, > leopard version. > > And now that I am looking at your previous email, it seems you were > running the freesurfer 5.1 leopard version in that case too. > > It also looks like you are indeed running a 32bit snow leopard machine > so please move (or completely erase) any previously installed version of > freesurfer you have on your machine and download and install this one. > > > > > -Zeke > > > On 12/04/2013 03:21 PM, Skyler Gabriel Shollenbarger wrote: >> Hi Zeke, >> >> Thanks for the help. We installed the 64bit version and got the same error. >> >> INFO: Distances between consecutive points in test subject's space are 5 5 6 >> 5 >> Writing output files to >> /BrainLabDocs/studies/nicotine_mj_ecstasy_study/data/MRI/N1064/data/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_* >> dmri_train(65940) malloc: *** mmap(size=159744) failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice >> >> Cannot allocate memory >> >> I've attached the error log for trac-all in case you need. >> >> Thanks again! >> Skyler and Jon >> >> >> - Original Message - >> From: "Z K" >> To: "Skyler Gabriel Shollenbarger" >> Cc: "Anastasia Yendiki" , >> freesurfer@nmr.mgh.harvard.edu >> Sent: Wednesday, December 4, 2013 9:46:37 AM >> Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts >> >> It looks like your running 32bit freesurfer on a 64bit machine with snow >> leopard installed on it. In this case You will have to install the 64bit >> version of freesurfer instead of the 32bit version you installed previously. >> >> You can get the version you need from the following link: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg >> >> Sorry for the confusion. >> >> -Zeke >> >> On 12/04/2013 10:34 AM, Skyler Gabriel Shollenbarger wrote: >>> Hi Anastasia, >>> >>> Thanks for y
[Freesurfer] qdec analysis with 2 covariates
HI freesurfer experts I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and 2 covariates(age and gender) to study the effect of these factors on cortical thickness. I can only select a covariate in the qdec gui. is there a way to select both covariates in the qdec GUI? Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] trac-all version 5.3 crash
Hi freesurfer experts, I've recnetly upgraded to freesurfer 5.3 (lion) 64bit version on our Mac Pro when I run trac-all -prep, I get the following error: writing to /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 > /Studies/MJMRI/MJ0030/freesurfer/dmri/dcminfo.dat Trace/BPT trap Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Dec 6 11:20:50 CST 2013 I've included the trac-all.log and trac-all.error file the trac-all log indicates in incompatible library version: Reason: Incompatible library version: mri_probedicom requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 I have reinstalled Xquartz and rebooted, but I still get the same error. what else can I do? system info: mac pro 6-core intel Xeon MAc OS 10.6.8 snowleopard Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219Fri Dec 6 11:19:30 CST 2013 /Studies/MJMRI/MJ0030 /Applications/freesurfer/bin/trac-all -c dmrirc_single_subject -prep Subject freesurfer SUBJECTS_DIR /Studies/MJMRI/MJ0030 FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 wieser psy-blackbird.ad.uwm.edu Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited descriptors 2560 memorylocked unlimited maxproc 266 PhysMem: 1343M wired, 1106M active, 2481M inactive, 4931M used, 19G free. Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:31-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200 FLIRT version 5.5 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:31-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:31-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-17:19:32-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: User: wieser Machine: psy-blackbird.ad.uwm.edu Platform: Darwin PlatformVersion: 10.8.0 CompilerName: GCC CompilerVersion: 40200 New invocation of trac-preproc wieser psy-blackbird.ad.uwm.edu Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited descriptors 2560 memorylocked unlimited maxproc 266 PhysMem: 1344M wired, 1107M active, 2481M inactive, 4932M used, 19G free. #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Fri Dec 6 11:19:33 CST 2013 mri_convert /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz mri_convert /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1... Starting DICOMRe
Re: [Freesurfer] qdec analysis with 2 covariates
thanks doug, We've run a 2x2 analysis for thickness in Qdec and want the get the average thickness value for each cluster, for each subject. How can i get a table of thickness data , for feach subject in the analysis Jon - Original Message - From: "Douglas N Greve" To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 9, 2013 1:48:15 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Hi Jon, QDEC does not currently allow more than one covariates of interest. You will have to use the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) doug On 12/05/2013 02:57 PM, Jon Wieser wrote: > HI freesurfer experts > > I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) > and 2 covariates(age and gender) to study the effect of these factors on > cortical thickness. I can only select a covariate in the qdec gui. is there > a way to select both covariates in the qdec GUI? > Thanks > Jon > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec analysis with 2 covariates
I found data for the average thickness all subjects for each cluster, but I haven't found the individual subject's thickness for each cluster. can you direct me to that data? Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Monday, December 9, 2013 2:15:39 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates It is in one of the output files. Look for the .dat file in mri_glmfit-sim --help On 12/09/2013 03:01 PM, Jon Wieser wrote: > thanks doug, > > We've run a 2x2 analysis for thickness in Qdec and want the get the average > thickness value for each cluster, for each subject. > How can i get a table of thickness data , for feach subject in the analysis > Jon > > - Original Message - > From: "Douglas N Greve" > To: freesurfer@nmr.mgh.harvard.edu > Sent: Monday, December 9, 2013 1:48:15 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > Hi Jon, QDEC does not currently allow more than one covariates of > interest. You will have to use the command-line stream (ie, > mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) > > doug > > > On 12/05/2013 02:57 PM, Jon Wieser wrote: >> HI freesurfer experts >> >> I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) >> and 2 covariates(age and gender) to study the effect of these factors on >> cortical thickness. I can only select a covariate in the qdec gui. is there >> a way to select both covariates in the qdec GUI? >> Thanks >> Jon >> -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec analysis with 2 covariates
i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the qdec output directory Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 1:42:37 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Is there a cache.mri_glmfit-sim.log in the output folder? Can you send it to me? Also, please remember to post to the list. thanks! doug On 12/10/2013 02:30 PM, Jon Wieser wrote: > FS version 5.3 > > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, December 10, 2013 1:05:26 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > hmmm, it should be there. What version of FS are you using? > > > > On 12/10/2013 12:57 PM, Jon Wieser wrote: >> i was getting the values for the command terminal, when I press the "find >> clusters and GOTo Max" button on the qdec GUI. >> there is no file named cache.th20.abs.y.dat or something similar. i did a >> "find" command to list all the *abs*.dat files in the directory >> >> qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >> qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat >> qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat >> qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat >> qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat >> qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >> qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat >> >> >> >> >> these files contain: >> >> # CSD PDF/CDF >> # simtype null-z >> # anattype surface fsaverage lh >> # FixGroupSubjectArea 1 >> # merged 0 >> # contrastNA >> # seed1271277527 >> # thresh 1.30 >> # threshsign 0.00 >> # searchspace 74612.965197 >> # nullfwhm15.00 >> # varfwhm -1.00 >> # nrepetitions 1 >> # NOTE: nreps and nrepetitions are both valid for volume data. >> # NOTE: nreps is invalid (-1) for surface data to assure. >> # NOTE: backwards INcompatibility. >> # $Id: volcluster.c,v 1.50.2.1 2011/03/28 15:32:36 greve Exp $ >> # nreps -1 >> # FixSurfClusterArea 1 >> # $Id: surfcluster.c,v 1.26.2.2 2011/11/10 16:01:11 greve Exp $ >> # nbins 100 >> # BinNo MaxClustBin MaxClustPDF MaxClustCDF GRFCDFMaxSigBin MaxSigPDF >> MaxSigCDF >> 0 204.826004 0.000500 0.999500 0.998289 2.456050 >> 0.000500 0.999500 >> 1 220.348267 0.001800 0.997700 0.996805 2.811329 >> 0.008100 0.991400 >> 2 235.870529 0.004300 0.993400 0.994388 3.166609 >> 0.022200 0.969200 >> 3 251.392792 0.007100 0.986300 0.990673 3.521888 >> 0.030300 0.938900 >> 4 266.915039 0.015600 0.970700 0.985251 3.877167 >> 0.028900 0.91 >> 5 282.437317 0.017500 0.953200 0.977702 4.232447 >> 0.022600 0.887400 >> 6 297.959595 0.021400 0.931800 0.967628 4.587726 >> 0.015200 0.872200 >> 7 313.481842 0.033600 0.898200 0.954689 4.943005 >> 0.012300 0.859900 >> 8 329.004089 0.036100 0.862100 0.938634 5.298285 >> 0.009800 0.850100 >> 9 344.526367 0.038000 0.824100 0.919325 5.653563 >> 0.007300 0.842800 >>10 360.048645 0.042500 0.781600 0.896747 6.008843 >> 0.009200 0.833600 >> 11 375.570892 0.05 0.731600 0.871009 6.364122 >> 0.006900 0.826700 >> 12 391.093140 0.043400 0.688200 0.842332 6.719401 >> 0.007100 0.819600 >> 13 406.615417 0.047300 0.640900 0.811034 7.074681 >> 0.005500 0.814100 >> 14 422.137695 0.050700 0.590200 0.777508 7.429960 >> 0.005500 0.808600 >> 15 437.659943 0.047400 0.542800 0.742195 7.785239 >> 0.005200 0.803400 >> 16 453.182190 0.044100 0.498700 0.705560 8.140518 >> 0.004900 0.798500 >> 17 468.704468 0.042700 0.456000 0.668070 8.495798 >> 0.005100 0.793400 >> 18 484.226746 0.040600 0.415400 0.630176 8.851077 >> 0.006100 0.787300 >> 19 499.748962 0.034900 0.380500 0.592300 9.206356 &
Re: [Freesurfer] qdec analysis with 2 covariates
thanks, I ran mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs MTA_ADHD_MJ is my project file and has the results from qdec in it it has produced: lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat these files have 120 rows. each row has a thickness value s example 2.71869 2.52448 2.50450 2.53677 2.58363 2.50404 2.42116 2.61757 2.51820 2.59009 2.42524 2.72043 2.59479 2.38014 2.41052 2.58483 2.49214 2.45870 2.51685 2.62981 2.59232 it appears that there is the thickness for each subject in the files I would like to have the thickness value, for each cluster, for every subject we have 120 subjects, with about 40 clusters Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Tuesday, December 10, 2013 2:30:31 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates OK, sorry, I thought qdec was running a script called mri_glmfit-sim but it appears to be running the correction internally. That means that you will have to run mri_glmfit-sim yourself, something like mri_glmfit-sim --glmdir glmdir --cache 1.3 abs doug On 12/10/2013 02:53 PM, Jon Wieser wrote: > i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the > qdec output directory > Jon > > > - Original Message ----- > From: "Douglas N Greve" > To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, December 10, 2013 1:42:37 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > Is there a cache.mri_glmfit-sim.log in the output folder? Can you send > it to me? Also, please remember to post to the list. thanks! > doug > > > On 12/10/2013 02:30 PM, Jon Wieser wrote: >> FS version 5.3 >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, December 10, 2013 1:05:26 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> hmmm, it should be there. What version of FS are you using? >> >> >> >> On 12/10/2013 12:57 PM, Jon Wieser wrote: >>> i was getting the values for the command terminal, when I press the "find >>> clusters and GOTo Max" button on the qdec GUI. >>> there is no file named cache.th20.abs.y.dat or something similar. i did a >>> "find" command to list all the *abs*.dat files in the directory >>> >>> qdec/MTA_ADHD_MJ/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>> qdec/MTA_ADHD_MJ/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th20.pdf.dat >>> qdec/Untitled/lh-Avg-thickness-Age-Cor/mc-z.abs.th13.pdf.dat >>> qdec/Untitled/lh-Avg-thickness-Gender-Cor/mc-z.abs.th13.pdf.dat >>> qdec/Untitled/lh-Diff-ADHD-nonADHD-Intercept-thickness/mc-z.abs.th13.pdf.dat >>> qdec/Untitled/lh-Diff-MJnonuser-MJuser-Intercept-thickness/mc-z.abs.th13.pdf.dat >>> qdec/Untitled/lh-X-ADHD-MJ_group-Intercept-thickness/mc-z.abs.th13.pdf.dat >>> >>> >>> >>> >>> these files contain: >>> >
Re: [Freesurfer] qdec analysis with 2 covariates
yes, that is what we want, but the files contain only 1-3 columns Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Tuesday, December 10, 2013 3:44:50 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates There should be a column for each cluster in contrast. Is that what you want? On 12/10/2013 04:37 PM, Jon Wieser wrote: > thanks, > I ran > mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs > > MTA_ADHD_MJ is my project file and has the results from qdec in it > > > it has produced: > > lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat > lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat > lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat > lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat > lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat > lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat > lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat > lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat > lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat > lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat > lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat > lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat > lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat > lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat > rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat > rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat > rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat > rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat > rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat > rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat > rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat > rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat > rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat > rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat > rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat > rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat > > > > these files have 120 rows. each row has a thickness value s > example > 2.71869 > 2.52448 > 2.50450 > 2.53677 > 2.58363 > 2.50404 > 2.42116 > 2.61757 > 2.51820 > 2.59009 > 2.42524 > 2.72043 > 2.59479 > 2.38014 > 2.41052 > 2.58483 > 2.49214 > 2.45870 > 2.51685 > 2.62981 > 2.59232 > > it appears that there is the thickness for each subject in the files > > I would like to have the thickness value, for each cluster, for every subject > > we have 120 subjects, with about 40 clusters > Jon > > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Tuesday, December 10, 2013 2:30:31 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > OK, sorry, I thought qdec was running a script called mri_glmfit-sim but > it appears to be running the correction internally. That means that you > will have to run mri_glmfit-sim yourself, something like > > mri_glmfit-sim --glmdir glmdir --cache 1.3 abs > > doug > > > On 12/10/2013 02:53 PM, Jon Wieser wrote: >> i have a mri_glmfit.log,(attached) but no cache.mri_glmfit-sim.log in the >> qdec output directory >> Jon >> >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, December 10, 2013 1:42:37 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> Is there a cache.mri_glmfit-sim.log in the output folder? Can you send >> it to me? Also, please remember to post to the list. thanks! >> doug >> >> >> On 12/10/2013 02:30 PM, Jon Wieser wrote: >>> FS version 5.3 >>> >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu >>> Sent: Tuesday, December 10, 2013 1:05:26 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> hmmm, it should be there. What version of FS are you using? >>> >>> >>> >>> On 12/10/2013 12:57 PM, Jon Wieser wrote: >>>> i was getting the values for the command terminal, when I press the "find >&g
Re: [Freesurfer] qdec analysis with 2 covariates
Hi Doug I'm looking at the effect of MJ usage, the effect of whetherthe subject has AHDH, and the interaction between MJ usage and ADHD our threshold is 1.3 i have attahced our qdec.table.dat file we are also looking at age and gender as covariates Jon Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:20:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates which contrast are you looking at in QDEC? Also, what is the voxel-wise threshold in QDEC? The value I gave in the command below is 1.3 but I got that from one of your CSD files. On 12/10/2013 05:10 PM, Jon Wieser wrote: > HI doug, > no, the summary files in the contrasts have the same # of cluster as the > columns in their OCN.dat \ > the 40 cluster are seen in qdec when I run the "find cluster" and Goto max" > button. most of these clusters go away in qdec when I run the montecarlo > simulation > > Jon > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Tuesday, December 10, 2013 4:03:06 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > So one of the contrasts has 40 clusters in the summary file but the > y.ocn.dat file only has a few columns? > > > On 12/10/2013 04:54 PM, Jon Wieser wrote: >> yes, that is what we want, but the files contain only 1-3 columns >> >> Jon >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" >> Cc: "freesurfer" >> Sent: Tuesday, December 10, 2013 3:44:50 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> There should be a column for each cluster in contrast. Is that what you >> want? >> >> >> On 12/10/2013 04:37 PM, Jon Wieser wrote: >>> thanks, >>> I ran >>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs >>> >>> MTA_ADHD_MJ is my project file and has the results from qdec in it >>> >>> >>> it has produced: >>> >>> lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>> lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>> rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> >>> >>> >>> these files have 120 rows. each row has a thickness value s >>> example >>>2.71869 >>>2.52448 >>>2.50450 >>>2.53677 >>>2.58363 >>>2.50404 >>>2.42116 >>>2.61757 >>>2.51820 >>>2.59009 >>>2.42524 >>>2.72043 >>>2.59479 >>>2.38014 >>>2.41052 >>>2.58483 >>>2.49214 >>>2.45870 >>>2.51685 >>> 2
Re: [Freesurfer] qdec analysis with 2 covariates
Is it possible to get the individual subject data for the clusters, before the monte carlo simulation has been run? I click "find clusters and goto max" . then on the command line it shows me the clusters stats and then when I click the "next" button under "Clusters". it shows me the graph of the thickness for each cluster, with thickness values for all subjects. is it possible to output the data values used to make the graph? Jon - Original Message - From: "Jon Wieser" To: "Douglas N Greve" Cc: "freesurfer" Sent: Tuesday, December 10, 2013 4:32:10 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Hi Doug I'm looking at the effect of MJ usage, the effect of whetherthe subject has AHDH, and the interaction between MJ usage and ADHD our threshold is 1.3 i have attahced our qdec.table.dat file we are also looking at age and gender as covariates Jon Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 10, 2013 4:20:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates which contrast are you looking at in QDEC? Also, what is the voxel-wise threshold in QDEC? The value I gave in the command below is 1.3 but I got that from one of your CSD files. On 12/10/2013 05:10 PM, Jon Wieser wrote: > HI doug, > no, the summary files in the contrasts have the same # of cluster as the > columns in their OCN.dat \ > the 40 cluster are seen in qdec when I run the "find cluster" and Goto max" > button. most of these clusters go away in qdec when I run the montecarlo > simulation > > Jon > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Tuesday, December 10, 2013 4:03:06 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > So one of the contrasts has 40 clusters in the summary file but the > y.ocn.dat file only has a few columns? > > > On 12/10/2013 04:54 PM, Jon Wieser wrote: >> yes, that is what we want, but the files contain only 1-3 columns >> >> Jon >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" >> Cc: "freesurfer" >> Sent: Tuesday, December 10, 2013 3:44:50 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> There should be a column for each cluster in contrast. Is that what you >> want? >> >> >> On 12/10/2013 04:37 PM, Jon Wieser wrote: >>> thanks, >>> I ran >>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs >>> >>> MTA_ADHD_MJ is my project file and has the results from qdec in it >>> >>> >>> it has produced: >>> >>> lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>> lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> lh-X-MJ_group-ADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>> rh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>> rh-X-MJ_group-ADHD-Intercept-thickness/cache.th
Re: [Freesurfer] qdec analysis with 2 covariates
oh, so it's showing the thickness values for one vertex in the cluster, not the average of all veretices in the cluster. we are interested in the average of the cluster Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Thursday, December 12, 2013 1:22:35 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates It is showing you scatter plots from individual vertices, not an average over the cluster doug On 12/12/2013 12:27 PM, Jon Wieser wrote: > Is it possible to get the individual subject data for the clusters, before > the monte carlo simulation has been run? > I click "find clusters and goto max" . then on the command line it shows > me the clusters stats and then when I click the "next" button under > "Clusters". it shows me the graph of the thickness for each cluster, with > thickness values for all subjects. is it possible to output the data values > used to make the graph? > Jon > > - Original Message - > From: "Jon Wieser" > To: "Douglas N Greve" > Cc: "freesurfer" > Sent: Tuesday, December 10, 2013 4:32:10 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > Hi Doug > I'm looking at the effect of MJ usage, the effect of whetherthe subject has > AHDH, and the interaction between MJ usage and ADHD > our threshold is 1.3 > > i have attahced our qdec.table.dat file > we are also looking at age and gender as covariates > Jon > > Jon > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, December 10, 2013 4:20:30 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > which contrast are you looking at in QDEC? Also, what is the voxel-wise > threshold in QDEC? The value I gave in the command below is 1.3 but I > got that from one of your CSD files. > > > On 12/10/2013 05:10 PM, Jon Wieser wrote: >> HI doug, >>no, the summary files in the contrasts have the same # of cluster as >> the columns in their OCN.dat \ >> the 40 cluster are seen in qdec when I run the "find cluster" and Goto max" >> button. most of these clusters go away in qdec when I run the montecarlo >> simulation >> >> Jon >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" >> Cc: "freesurfer" >> Sent: Tuesday, December 10, 2013 4:03:06 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> So one of the contrasts has 40 clusters in the summary file but the >> y.ocn.dat file only has a few columns? >> >> >> On 12/10/2013 04:54 PM, Jon Wieser wrote: >>> yes, that is what we want, but the files contain only 1-3 columns >>> >>> Jon >>> >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Jon Wieser" >>> Cc: "freesurfer" >>> Sent: Tuesday, December 10, 2013 3:44:50 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> There should be a column for each cluster in contrast. Is that what you >>> want? >>> >>> >>> On 12/10/2013 04:37 PM, Jon Wieser wrote: >>>> thanks, >>>> I ran >>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs >>>> >>>> MTA_ADHD_MJ is my project file and has the results from qdec in it >>>> >>>> >>>> it has produced: >>>> >>>> lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>>> lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.dat >>>> lh-Diff-ADHD-nonADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> lh-Diff-ADHD-nonADHD-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> lh-Diff-ADHD-nonADHD-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> lh-Diff-MJnonuser-MJuser-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> lh-Diff-MJnonuser-MJuser-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> lh-X-ADHD-MJ_group-Cor-thickness-Gender/cache.th13.abs.y.ocn.dat >>>> lh-X-ADHD-MJ_group-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>> lh-X-MJ_group-ADHD-Cor-thickness-Age/cache.th13.abs.y.ocn.dat >>>> lh-X-MJ_group-ADHD-Cor-thickness-Gender/cache.th13.abs.
Re: [Freesurfer] qdec analysis with 2 covariates
HI Doug MRI_glmfit-sim didn't recognize the --cwd option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 ERROR: Flag --cwd unrecognized. --glmdir MTA_ADHD_MJ --cwd .99 - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, December 13, 2013 10:54:19 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I'm sure that those clusters are not very significant. Try running mri_glmfit-sim with --cwd .99 to capture all clusters doug On 12/12/2013 03:27 PM, Jon Wieser wrote: > HI Doug, > here's a screen shot, showing the clusters and a scatter plot for one of the > 45 clusters. > for this dataset, ussualy there is 0 or 1 clusters after monte carlo > simulation. i'm not sure if they match one of the 45 clusters in qdec. i'l > have to look into that. > > I would like to have a file which contains the data represented in the > scatter plot, for all of the 45 clusters, vlaues of thickness for each > subject. is that possible? > I tried runnin mri_surfcluster, but it only gave me the average data for that > clusters, not the individual data. > > thanks! > > Jon > > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Thursday, December 12, 2013 1:15:58 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > I'm not sure what is going on. Can you send a screen shot of the qdec > window when you see 40 clusters? It might be that it is showing clusters > regardless of the cluster significance. Do the 3 or 4 clusters created > when you run mri_glmfit-sim match clusters in qdec? > > On 12/10/2013 05:32 PM, Jon Wieser wrote: >> Hi Doug >> I'm looking at the effect of MJ usage, the effect of whetherthe subject >> has AHDH, and the interaction between MJ usage and ADHD >> our threshold is 1.3 >> >> i have attahced our qdec.table.dat file >> we are also looking at age and gender as covariates >> Jon >> >> Jon >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, December 10, 2013 4:20:30 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> which contrast are you looking at in QDEC? Also, what is the voxel-wise >> threshold in QDEC? The value I gave in the command below is 1.3 but I >> got that from one of your CSD files. >> >> >> On 12/10/2013 05:10 PM, Jon Wieser wrote: >>> HI doug, >>> no, the summary files in the contrasts have the same # of cluster as >>> the columns in their OCN.dat \ >>> the 40 cluster are seen in qdec when I run the "find cluster" and Goto >>> max" button. most of these clusters go away in qdec when I run the >>> montecarlo simulation >>> >>> Jon >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Jon Wieser" >>> Cc: "freesurfer" >>> Sent: Tuesday, December 10, 2013 4:03:06 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> So one of the contrasts has 40 clusters in the summary file but the >>> y.ocn.dat file only has a few columns? >>> >>> >>> On 12/10/2013 04:54 PM, Jon Wieser wrote: >>>> yes, that is what we want, but the files contain only 1-3 columns >>>> >>>> Jon >>>> >>>> - Original Message - >>>> From: "Douglas N Greve" >>>> To: "Jon Wieser" >>>> Cc: "freesurfer" >>>> Sent: Tuesday, December 10, 2013 3:44:50 PM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> There should be a column for each cluster in contrast. Is that what you >>>> want? >>>> >>>> >>>> On 12/10/2013 04:37 PM, Jon Wieser wrote: >>>>> thanks, >>>>> I ran >>>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 1.3 abs >>>>> >>>>> MTA_ADHD_MJ is my project file and has the results from qdec in it >>>>> >>>>> >>>>> it has produced: >>>>> >>>>> lh-Avg-Intercept-thickness/cache.th13.abs.y.ocn.dat >>>>> lh-Avg-thickness-Age-Cor/cache.th13.abs.y.ocn.dat >>>>> lh-Avg-thickness-Gender-Cor/cache.th13.abs.y.ocn.d
Re: [Freesurfer] qdec analysis with 2 covariates
Hi doug it's requesting the --sim option mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 ERROR: must spec --sim mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim ERROR: flag --sim requires four arguments what args do I give the --sim! Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, December 13, 2013 11:18:49 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates sorry, it is --cwp On 12/13/2013 12:12 PM, Jon Wieser wrote: > HI Doug > MRI_glmfit-sim didn't recognize the --cwd option > > > mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 > ERROR: Flag --cwd unrecognized. > --glmdir MTA_ADHD_MJ --cwd .99 > > > > > > > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Friday, December 13, 2013 10:54:19 AM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > I'm sure that those clusters are not very significant. Try running > mri_glmfit-sim with --cwd .99 to capture all clusters > doug > > > On 12/12/2013 03:27 PM, Jon Wieser wrote: >> HI Doug, >> here's a screen shot, showing the clusters and a scatter plot for one of the >> 45 clusters. >> for this dataset, ussualy there is 0 or 1 clusters after monte carlo >> simulation. i'm not sure if they match one of the 45 clusters in qdec. i'l >> have to look into that. >> >> I would like to have a file which contains the data represented in the >> scatter plot, for all of the 45 clusters, vlaues of thickness for each >> subject. is that possible? >> I tried runnin mri_surfcluster, but it only gave me the average data for >> that clusters, not the individual data. >> >> thanks! >> >> Jon >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" >> Cc: "freesurfer" >> Sent: Thursday, December 12, 2013 1:15:58 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> I'm not sure what is going on. Can you send a screen shot of the qdec >> window when you see 40 clusters? It might be that it is showing clusters >> regardless of the cluster significance. Do the 3 or 4 clusters created >> when you run mri_glmfit-sim match clusters in qdec? >> >> On 12/10/2013 05:32 PM, Jon Wieser wrote: >>> Hi Doug >>> I'm looking at the effect of MJ usage, the effect of whetherthe subject >>> has AHDH, and the interaction between MJ usage and ADHD >>> our threshold is 1.3 >>> >>> i have attahced our qdec.table.dat file >>> we are also looking at age and gender as covariates >>> Jon >>> >>> Jon >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu >>> Sent: Tuesday, December 10, 2013 4:20:30 PM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> which contrast are you looking at in QDEC? Also, what is the voxel-wise >>> threshold in QDEC? The value I gave in the command below is 1.3 but I >>> got that from one of your CSD files. >>> >>> >>> On 12/10/2013 05:10 PM, Jon Wieser wrote: >>>> HI doug, >>>> no, the summary files in the contrasts have the same # of cluster >>>> as the columns in their OCN.dat \ >>>> the 40 cluster are seen in qdec when I run the "find cluster" and Goto >>>> max" button. most of these clusters go away in qdec when I run the >>>> montecarlo simulation >>>> >>>> Jon >>>> - Original Message - >>>> From: "Douglas N Greve" >>>> To: "Jon Wieser" >>>> Cc: "freesurfer" >>>> Sent: Tuesday, December 10, 2013 4:03:06 PM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> So one of the contrasts has 40 clusters in the summary file but the >>>> y.ocn.dat file only has a few columns? >>>> >>>> >>>> On 12/10/2013 04:54 PM, Jon Wieser wrote: >>>>> yes, that is what we want, but the files contain only 1-3 columns >>>>> >>>>> Jon >>>>> >>>>> - Original Message - >>>>> From: "Douglas N Greve" >>>>> To: &qu
Re: [Freesurfer] qdec analysis with 2 covariates
Hi Doug I ran : mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9 I have attached three of the output summary files Can you please confirm how to assess the cluster-wise p-value? Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu Sent: Friday, December 13, 2013 12:12:01 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates I would have thought that it would have gotten all of them. You can try something like --cwp .9 On 12/13/2013 01:03 PM, Jon Wieser wrote: > HI doug > thanks, that worked. it captured from 3-13 clusters for each contrast, > not quite the 30-45 that I was seeing in the GUI. > perhaps theses are the most significant clusters? > Jon > > - Original Message ----- > From: "Douglas N Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Friday, December 13, 2013 11:43:29 AM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > use the command I gave you before just add --cwp .99 to it > doug > > > On 12/13/2013 12:25 PM, Jon Wieser wrote: >> Hi doug >> it's requesting the --sim option >> >>mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 >> ERROR: must spec --sim >> >> >> >>mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim >> ERROR: flag --sim requires four arguments >> >> >> what args do I give the --sim! >> >> Jon >> >> >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" >> Cc: "freesurfer" >> Sent: Friday, December 13, 2013 11:18:49 AM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> sorry, it is --cwp >> >> On 12/13/2013 12:12 PM, Jon Wieser wrote: >>> HI Doug >>> MRI_glmfit-sim didn't recognize the --cwd option >>> >>> >>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 >>> ERROR: Flag --cwd unrecognized. >>> --glmdir MTA_ADHD_MJ --cwd .99 >>> >>> >>> >>> >>> >>> >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Jon Wieser" >>> Cc: "freesurfer" >>> Sent: Friday, December 13, 2013 10:54:19 AM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> I'm sure that those clusters are not very significant. Try running >>> mri_glmfit-sim with --cwd .99 to capture all clusters >>> doug >>> >>> >>> On 12/12/2013 03:27 PM, Jon Wieser wrote: >>>> HI Doug, >>>> here's a screen shot, showing the clusters and a scatter plot for one of >>>> the 45 clusters. >>>> for this dataset, ussualy there is 0 or 1 clusters after monte carlo >>>> simulation. i'm not sure if they match one of the 45 clusters in qdec. >>>> i'l have to look into that. >>>> >>>> I would like to have a file which contains the data represented in the >>>> scatter plot, for all of the 45 clusters, vlaues of thickness for each >>>> subject. is that possible? >>>> I tried runnin mri_surfcluster, but it only gave me the average data for >>>> that clusters, not the individual data. >>>> >>>> thanks! >>>> >>>> Jon >>>> >>>> - Original Message - >>>> From: "Douglas N Greve" >>>> To: "Jon Wieser" >>>> Cc: "freesurfer" >>>> Sent: Thursday, December 12, 2013 1:15:58 PM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> I'm not sure what is going on. Can you send a screen shot of the qdec >>>> window when you see 40 clusters? It might be that it is showing clusters >>>> regardless of the cluster significance. Do the 3 or 4 clusters created >>>> when you run mri_glmfit-sim match clusters in qdec? >>>> >>>> On 12/10/2013 05:32 PM, Jon Wieser wrote: >>>>> Hi Doug >>>>> I'm looking at the effect of MJ usage, the effect of whetherthe subject >>>>> has AHDH, and the interaction between MJ usage and ADHD >>>>> our threshold is 1.3 >>>>> >>>>> i have attahced our qdec.table.dat file >>>>> we are also looking at age and gender as covariates >>>>>
Re: [Freesurfer] qdec analysis with 2 covariates
so in the following cluster, the cluster-wise p-value is 0.80130? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot 1 3.247 90900134.66-37.1 -33.2 -24.5 0.80130 0.79620 0.80640 267 fusiform - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Monday, December 16, 2013 4:28:30 PM Subject: Re: [Freesurfer] qdec analysis with 2 covariates look at the CWP column doug On 12/16/2013 05:14 PM, Jon Wieser wrote: > Hi Doug > > I ran : > mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9 > > I have attached three of the output summary files > > Can you please confirm how to assess the cluster-wise p-value? > > Jon > > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu > Sent: Friday, December 13, 2013 12:12:01 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > > I would have thought that it would have gotten all of them. You can try > something like --cwp .9 > > > On 12/13/2013 01:03 PM, Jon Wieser wrote: >> HI doug >> thanks, that worked. it captured from 3-13 clusters for each contrast, >> not quite the 30-45 that I was seeing in the GUI. >> perhaps theses are the most significant clusters? >> Jon >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" >> Cc: "freesurfer" >> Sent: Friday, December 13, 2013 11:43:29 AM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> use the command I gave you before just add --cwp .99 to it >> doug >> >> >> On 12/13/2013 12:25 PM, Jon Wieser wrote: >>> Hi doug >>> it's requesting the --sim option >>> >>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 >>> ERROR: must spec --sim >>> >>> >>> >>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim >>> ERROR: flag --sim requires four arguments >>> >>> >>> what args do I give the --sim! >>> >>> Jon >>> >>> >>> >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Jon Wieser" >>> Cc: "freesurfer" >>> Sent: Friday, December 13, 2013 11:18:49 AM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> sorry, it is --cwp >>> >>> On 12/13/2013 12:12 PM, Jon Wieser wrote: >>>> HI Doug >>>> MRI_glmfit-sim didn't recognize the --cwd option >>>> >>>> >>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 >>>> ERROR: Flag --cwd unrecognized. >>>> --glmdir MTA_ADHD_MJ --cwd .99 >>>> >>>> >>>> >>>> >>>> >>>> >>>> - Original Message - >>>> From: "Douglas N Greve" >>>> To: "Jon Wieser" >>>> Cc: "freesurfer" >>>> Sent: Friday, December 13, 2013 10:54:19 AM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> >>>> I'm sure that those clusters are not very significant. Try running >>>> mri_glmfit-sim with --cwd .99 to capture all clusters >>>> doug >>>> >>>> >>>> On 12/12/2013 03:27 PM, Jon Wieser wrote: >>>>> HI Doug, >>>>> here's a screen shot, showing the clusters and a scatter plot for one of >>>>> the 45 clusters. >>>>> for this dataset, ussualy there is 0 or 1 clusters after monte carlo >>>>> simulation. i'm not sure if they match one of the 45 clusters in qdec. >>>>> i'l have to look into that. >>>>> >>>>> I would like to have a file which contains the data represented in the >>>>> scatter plot, for all of the 45 clusters, vlaues of thickness for each >>>>> subject. is that possible? >>>>> I tried runnin mri_surfcluster, but it only gave me the average data for >>>>> that clusters, not the individual data. >>>>> >>>>> thanks! >>>>> >>>>> Jon >>>>> >>>>> - Original Message - >>>>> From: "Douglas N Greve" >>>>> To: "Jon Wieser" >>>
[Freesurfer] mri_glmfit-sim Error
After running a group comparison using qdec I wanted to use mc-z for multiple comparison correction I tried running: mri_glmfit-sim \ --glmdir MTA_ADHD_MJ2 \ --sim mc-z 1000 2.0 mc-z.negative \ --sim-sign abs --cwpvalthresh 0.999 \ --overwrite ERROR: dimension mismatch between X and contrast MTA_ADHD_MJ2/tmp.mri_glmfit-sim-9440/lh-Avg-thickness-Age-Cor.mtx X has 4 cols, C has 8 cols What does this mean and how to fix it? -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] qdec analysis with 2 covariates
I would think that a p-value of 0.8013 is very insignificant. Am I missing somthing? Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Tuesday, December 17, 2013 10:46:36 AM Subject: Re: [Freesurfer] qdec analysis with 2 covariates Yes, with a 95% confidence range of .7962 to .8065 doug On 12/17/2013 11:04 AM, Jon Wieser wrote: > so in the following cluster, the cluster-wise p-value is 0.80130? > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow > CWPHi NVtxs Annot > 1 3.247 90900134.66-37.1 -33.2 -24.5 0.80130 0.79620 > 0.80640 267 fusiform > > > - Original Message - > From: "Douglas N Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Monday, December 16, 2013 4:28:30 PM > Subject: Re: [Freesurfer] qdec analysis with 2 covariates > > look at the CWP column > doug > > On 12/16/2013 05:14 PM, Jon Wieser wrote: >> Hi Doug >> >> I ran : >> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9 >> >> I have attached three of the output summary files >> >> Can you please confirm how to assess the cluster-wise p-value? >> >> Jon >> >> - Original Message - >> From: "Douglas N Greve" >> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu >> Sent: Friday, December 13, 2013 12:12:01 PM >> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >> >> >> I would have thought that it would have gotten all of them. You can try >> something like --cwp .9 >> >> >> On 12/13/2013 01:03 PM, Jon Wieser wrote: >>> HI doug >>> thanks, that worked. it captured from 3-13 clusters for each contrast, >>> not quite the 30-45 that I was seeing in the GUI. >>> perhaps theses are the most significant clusters? >>> Jon >>> >>> - Original Message - >>> From: "Douglas N Greve" >>> To: "Jon Wieser" >>> Cc: "freesurfer" >>> Sent: Friday, December 13, 2013 11:43:29 AM >>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>> >>> >>> use the command I gave you before just add --cwp .99 to it >>> doug >>> >>> >>> On 12/13/2013 12:25 PM, Jon Wieser wrote: >>>> Hi doug >>>> it's requesting the --sim option >>>> >>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 >>>> ERROR: must spec --sim >>>> >>>> >>>> >>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwp .99 --sim >>>> ERROR: flag --sim requires four arguments >>>> >>>> >>>> what args do I give the --sim! >>>> >>>> Jon >>>> >>>> >>>> >>>> - Original Message - >>>> From: "Douglas N Greve" >>>> To: "Jon Wieser" >>>> Cc: "freesurfer" >>>> Sent: Friday, December 13, 2013 11:18:49 AM >>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>> >>>> sorry, it is --cwp >>>> >>>> On 12/13/2013 12:12 PM, Jon Wieser wrote: >>>>> HI Doug >>>>> MRI_glmfit-sim didn't recognize the --cwd option >>>>> >>>>> >>>>> mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99 >>>>> ERROR: Flag --cwd unrecognized. >>>>> --glmdir MTA_ADHD_MJ --cwd .99 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> - Original Message - >>>>> From: "Douglas N Greve" >>>>> To: "Jon Wieser" >>>>> Cc: "freesurfer" >>>>> Sent: Friday, December 13, 2013 10:54:19 AM >>>>> Subject: Re: [Freesurfer] qdec analysis with 2 covariates >>>>> >>>>> >>>>> I'm sure that those clusters are not very significant. Try running >>>>> mri_glmfit-sim with --cwd .99 to capture all clusters >>>>> doug >>>>> >>>>> >>>>> On 12/12/2013 03:27 PM, Jon Wieser wrote: >>>>>> HI Doug, >>>>>> here's a screen shot, showing the clusters and a scatter plot for one of >>>>>> the 45 clusters. >>>>&g
[Freesurfer] POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION; UNIVERSITY OF WISCONSIN-MILWAUKEE
POST-DOCTORAL POSITION IN NEUROIMAGING, NEUROPSYCHOLOGY AND ADDICTION; UNIVERSITY OF WISCONSIN-MILWAUKEE. Sponsor: Krista Lisdahl, Ph.D. A Postdoctoral Fellow position at the University of Wisconsin-Milwaukee (UWM), Psychology Department (http://www4.uwm.edu/letsci/psychology/) will be available starting September 2014 (start date is negotiable). Neuroimaging (fMRI, DTI) will be conducted at the Medical College of Wisconsin’s (MCW) world-renowned Center for Imaging Research (http://www.mcw.edu/biophysics/mri/cir.htm). Dr. Krista Lisdahl, a licensed clinical neuropsychologist with specialization in addiction and neuroimaging, will supervise the fellowship. The objective of this NIH-funded research is characterize the effects of marijuana (MJ) use on frontolimbic brain structure, functioning and connectivity in youth by the creation of IDEAA (Imaging Data in Emerging Adults with Addiction), a multi-site consortium comprised of investigators (Drs. Krista Lisdahl, Staci Gruber, Susan Tapert, Francesca Filbey) using common, overlapping neuroimaging and behavioral measures in over 600 MJ-using and healthy control adolescents and emerging adults. Other areas of study within the laboratory include chronic effects of alcohol/binge drinking, MJ, nicotine and ecstasy use on neurocognition; healthy adolescent and emerging adult neurodevelopment; imaging genetics; multi-modal neuroimaging research methods; effects of exercise and body fat on neurocognition; and neuropsychological measurement. Collaborative opportunities and rich didactic experiences at UWM and MCW are available within a wide range of disciplines, especially affective neuroscience, cognitive rehabilitation, clinical neuropsychology, and exercise science. Clinical Experience. Opportunities for supervised clinical neuropsychology work may be arranged at UWM, MCW or the Milwaukee VA for students interested in ABPP-CN certification. However, this is not an official part of the postdoc. Funding: The position will be funded by Dr. Lisdahl’s NIDA grants. Duties will include: processing and analyzing MRI data; completing neuropsychological assessments; managing research assistants; manuscript and grant preparation. Travel funding to conferences will be available. Requirements include: Ph.D. in psychology, neuroscience or related discipline with strong interest in developing research career in addiction neuroscience or adolescent neurodevelopment. Experience with fMRI/DTI-related research methods (e-prime programming; AFNI, Freesurfer, FSL processing; fcMRI analysis methods) are preferred. Position is available for 1 year with the option of extending up to 3 years, depending upon performance and mutual interest. To apply please send cover letter, CV, statement of research interests and goals, and 3 letters of reference to Dr. Krista Lisdahl (krista.med...@gmail.com). Applications due July 2014, but will be reviewed on a rolling basis. UWM and Dr. Lisdahl strongly value diversity and are committed to equal opportunity in employment. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: trac-all -prep error
the dmri_train command is giving a segmentation fault. how can I fix this? Jon - Original Message - From: "Jon Wieser" To: "freesurfer" Sent: Wednesday, January 8, 2014 2:23:34 PM Subject: [Freesurfer] Fwd: trac-all -prep error Hello I'm getting the following error when running trac-all -c dmrirc -prep INFO: Distances between consecutive points in test subject's space are 7 9 7 8 WARN: Could not find satisfactory control point fit - try 809 Writing output files to /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_* Writing spline volume to /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_cpts_5.nii.gz Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Wed Jan 8 12:07:54 CST 2014 i'm running traclua 5.3 attached are the trac-all.log and trac-ll.error files -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: trac-all -path error
dmri_paths is producing a segmentation fault. How can I fix this? thanks JOn - Original Message - From: "Jon Wieser" To: "freesurfer" Sent: Wednesday, January 8, 2014 11:54:55 AM Subject: [Freesurfer] Fwd: trac-all -path error Dear freesurfer experts I'm getting the following error when runing trac-all -c dmrirc_single_subject -path Loading initial proposal SD's from /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt Processing pathway 3 of 18... Initializing MCMC Segmentation fault Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 I have attached the trac-all.log and trac-all.error files I am running tracula 5.3 -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: trac-all -path error
Hi Anastasia, I din't see anything missing from the brainmask or aparc+seg. I sent you the brainmask and aparc+seg files did you find anything wrong. if not, what else could cause the segmentatino fault? Thanks - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, January 10, 2014 6:15:23 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? Anything missing there that might affect the left ILF? a.y On Wed, 8 Jan 2014, Jon Wieser wrote: > > Dear freesurfer experts > I'm getting the following error when runing trac-all -c dmrirc_single_subject > -path > > > Loading initial proposal SD's from > /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt > Processing pathway 3 of 18... > Initializing MCMC > Segmentation fault > Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 > 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > I have attached the trac-all.log and trac-all.error files > > I am running tracula 5.3 > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: trac-all -prep error
Hi Anastasia, I didn't see anything blatently wrong with the apar+aseg or the DWI's. Can you be more specific as to what I should be looking for Thanks! Jon - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, January 10, 2014 6:16:56 PM Subject: Re: [Freesurfer] Fwd: trac-all -prep error Hi Jon - Again I'd look at this subject's aparc+aseg, as well as the DWIs themselves to see if there's anything going on that might affect the left ILF. a.y On Wed, 8 Jan 2014, Jon Wieser wrote: > > > Hello > I'm getting the following error when running trac-all -c dmrirc -prep > > INFO: Distances between consecutive points in test subject's space are 7 9 7 8 > WARN: Could not find satisfactory control point fit - try 809 > Writing output files to > /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_* > Writing spline volume to > /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_cpts_5.nii.gz > Segmentation fault > Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 > 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 > > trac-preproc exited with ERRORS at Wed Jan 8 12:07:54 CST 2014 > > > i'm running traclua 5.3 > > attached are the trac-all.log and trac-ll.error files > > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Fwd: trac-all -path error
Hi Anastasia, I didn't see anything missing from the brainmask or aparc+seg. I sent you the brainmask and aparc+seg files did you find anything wrong. if not, what else could cause the segmentatino fault? Thanks - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, January 10, 2014 6:15:23 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? Anything missing there that might affect the left ILF? a.y On Wed, 8 Jan 2014, Jon Wieser wrote: > > Dear freesurfer experts > I'm getting the following error when runing trac-all -c dmrirc_single_subject > -path > > > Loading initial proposal SD's from > /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt > Processing pathway 3 of 18... > Initializing MCMC > Segmentation fault > Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 > 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 > > > I have attached the trac-all.log and trac-all.error files > > I am running tracula 5.3 > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Fwd: trac-all -prep error
- Forwarded Message - From: "Jon Wieser" To: "Anastasia Yendiki" Cc: "freesurfer" Sent: Wednesday, January 22, 2014 10:10:19 AM Subject: Re: [Freesurfer] Fwd: trac-all -prep error Hi Anastasia, I didn't see anything blatently wrong with the apar+aseg or the DWI's. Can you be more specific as to what I should be looking for Thanks! Jon - Original Message ----- From: "Anastasia Yendiki" To: "Jon Wieser" Cc: "freesurfer" Sent: Friday, January 10, 2014 6:16:56 PM Subject: Re: [Freesurfer] Fwd: trac-all -prep error Hi Jon - Again I'd look at this subject's aparc+aseg, as well as the DWIs themselves to see if there's anything going on that might affect the left ILF. a.y On Wed, 8 Jan 2014, Jon Wieser wrote: > > > Hello > I'm getting the following error when running trac-all -c dmrirc -prep > > INFO: Distances between consecutive points in test subject's space are 7 9 7 8 > WARN: Could not find satisfactory control point fit - try 809 > Writing output files to > /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_* > Writing spline volume to > /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1096/data/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_bbr_cpts_5.nii.gz > Segmentation fault > Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 > 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 > > trac-preproc exited with ERRORS at Wed Jan 8 12:07:54 CST 2014 > > > i'm running traclua 5.3 > > attached are the trac-all.log and trac-ll.error files > > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: trac-all -path error
Hi Anastasia, We used both flirt and bbr registration in the dmrirc file, the Aparc+seg I just showedd you was from the BBR resitration. I looked at the flirt registration. it looks OK. should I rerun tracula using only the flirt registration? Jon - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Cc: "freesurfer" Sent: Thursday, February 6, 2014 11:00:25 AM Subject: Re: [Freesurfer] Fwd: trac-all -path error So there's your culprit. You need to fix the intra-subject (diffusion-to-T1) registration. Did you use flirt or bbregister for that? On Thu, 6 Feb 2014, Jon Wieser wrote: > Hi Anastasia, > I looked at the dlabel/diff/Aparc+aseg overlayed on the dmri/dtifit_FA.nii.gz > the alignemenst is way off (in freeview, in the coronal view, the aparc+seg > is rotated 45 degrees anti-clockwise), and parts of the FA map in the L ILF > area are missing. the original DTI is not missing data in these areas. I > have attached screenshots > Jon > > > > - Original Message - > From: "Anastasia Yendiki" > To: "Jon Wieser" > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, February 5, 2014 6:35:12 PM > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > Hi Jon - You need to look at the aparc+aseg after it has been mapped to > diffusion space. It's possible that it looks fine in its original space > but then maybe something goes wrong with the registration. So you should > look at the aparc+aseg and aparc+aseg_mask files from the tracula > dlabel/diff directory. These are in diffusion space and you can overlay > them on the FA map to see if there's anything strange in the ILF area. > > Hope this helps, > a.y > > On Tue, 14 Jan 2014, Jon Wieser wrote: > >> Hi anastasia >> I looked at the brainmask and the aparc+aseg. I did see anything missing >> in the area of the left ILF. >> I have attached the files. can you take a look at them? >> Thanks >> JOn >> >> - Original Message - >> From: "Anastasia Yendiki" >> To: "Jon Wieser" >> Cc: "freesurfer" >> Sent: Friday, January 10, 2014 6:15:23 PM >> Subject: Re: [Freesurfer] Fwd: trac-all -path error >> >> >> Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? >> Anything missing there that might affect the left ILF? >> >> a.y >> >> On Wed, 8 Jan 2014, Jon Wieser wrote: >> >>> >>> Dear freesurfer experts >>> I'm getting the following error when runing trac-all -c >>> dmrirc_single_subject -path >>> >>> >>> Loading initial proposal SD's from >>> /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt >>> Processing pathway 3 of 18... >>> Initializing MCMC >>> Segmentation fault >>> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 >>> 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >>> >>> >>> I have attached the trac-all.log and trac-all.error files >>> >>> I am running tracula 5.3 >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: trac-all -path error
Hi Anastasia, thanks for the information.we are able to process the DTI data successfully. we had 24 subjects which crashed during either the -perp or -path stage. I viewed the alignments between the FA and the alignement segmentations (flirt and bbr alignments), which ever alignment is better. I modify the dmrirc file to use that alignment and rerun trac-all , starting at the -prep stage all but 2 were successfuly processed with my method, that the dti tracts look good in freeview i didn't realign the registration using tkregister, because the anatomies are poor and lo res, making this realignment difficult thanks again! JOn - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 6, 2014 3:16:16 PM Subject: Re: [Freesurfer] Fwd: trac-all -path error We've generally seen better results with BBR, which is why it became the default setting. On Thu, 6 Feb 2014, Jon Wieser wrote: > HI Anastasia, > > I ran it again with the flirt registration and it finished ok. > We did not have a specific reason for running it both ways. we are using the > default setting for the dmrirc file. > do you recommend one method over the other? > > thanks again > Jon > > ----- Original Message - > From: "Anastasia Yendiki" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Thursday, February 6, 2014 3:07:12 PM > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > That's entirely up to you, and whether you had a specific reason for > running it both ways. > > If you want to fix the bbr registration manually, check the trac-all.log > file for a command at the end of bbregister, where it says "To check > results, run". > > On Thu, 6 Feb 2014, Jon Wieser wrote: > >> Hi Anastasia, >> We used both flirt and bbr registration in the dmrirc file, the Aparc+seg >> I just showedd you was from the BBR resitration. I looked at the flirt >> registration. it looks OK. >> should I rerun tracula using only the flirt registration? >> Jon >> >> - Original Message - >> From: "Anastasia Yendiki" >> To: "Jon Wieser" >> Cc: "freesurfer" >> Sent: Thursday, February 6, 2014 11:00:25 AM >> Subject: Re: [Freesurfer] Fwd: trac-all -path error >> >> >> So there's your culprit. You need to fix the intra-subject >> (diffusion-to-T1) registration. Did you use flirt or bbregister for that? >> >> On Thu, 6 Feb 2014, Jon Wieser wrote: >> >>> Hi Anastasia, >>> I looked at the dlabel/diff/Aparc+aseg overlayed on the >>> dmri/dtifit_FA.nii.gz >>> the alignemenst is way off (in freeview, in the coronal view, the aparc+seg >>> is rotated 45 degrees anti-clockwise), and parts of the FA map in the L >>> ILF area are missing. the original DTI is not missing data in these areas. >>> I have attached screenshots >>> Jon >>> >>> >>> >>> - Original Message - >>> From: "Anastasia Yendiki" >>> To: "Jon Wieser" >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Sent: Wednesday, February 5, 2014 6:35:12 PM >>> Subject: Re: [Freesurfer] Fwd: trac-all -path error >>> >>> >>> Hi Jon - You need to look at the aparc+aseg after it has been mapped to >>> diffusion space. It's possible that it looks fine in its original space >>> but then maybe something goes wrong with the registration. So you should >>> look at the aparc+aseg and aparc+aseg_mask files from the tracula >>> dlabel/diff directory. These are in diffusion space and you can overlay >>> them on the FA map to see if there's anything strange in the ILF area. >>> >>> Hope this helps, >>> a.y >>> >>> On Tue, 14 Jan 2014, Jon Wieser wrote: >>> >>>> Hi anastasia >>>> I looked at the brainmask and the aparc+aseg. I did see anything missing >>>> in the area of the left ILF. >>>> I have attached the files. can you take a look at them? >>>> Thanks >>>> JOn >>>> >>>> - Original Message - >>>> From: "Anastasia Yendiki" >>>> To: "Jon Wieser" >>>> Cc: "freesurfer" >>>> Sent: Friday, January 10, 2014 6:15:23 PM >>>> Subject: Re: [Freesurfer] Fwd: trac-all -path error >>>> >>>> >>>> Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? >>>&g
[Freesurfer] trac-all -prep exited with errors
Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt Image Exception : #23 :: Failed to open volume /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt for writing terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Fri Mar 22 11:41:39 CDT 2013 -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] trackstats2table error
I am trying to convert my dti tracts stats to a table and got the following error tractstats2table --inputs fmajor_PP_avg23_mni_flt/pathstats.overall.txt --overall --tablefile table.txt Traceback (most recent call last): File "/usr/local/freesurfer/bin/tractstats2table", line 9, in from fsutils import TractOverallStatsParser, TractByvoxelStatsParser, BadFileError, tractlogger ImportError: cannot import name TractOverallStatsParser -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trackstats2table error
i fixed the problem - Original Message - From: "Jon Wieser" To: "freesurfer" Sent: Tuesday, March 26, 2013 4:21:35 PM Subject: [Freesurfer] trackstats2table error I am trying to convert my dti tracts stats to a table and got the following error tractstats2table --inputs fmajor_PP_avg23_mni_flt/pathstats.overall.txt --overall --tablefile table.txt Traceback (most recent call last): File "/usr/local/freesurfer/bin/tractstats2table", line 9, in from fsutils import TractOverallStatsParser, TractByvoxelStatsParser, BadFileError, tractlogger ImportError: cannot import name TractOverallStatsParser -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tractstats@table output oddity
I ran tractstats2table to make a table of my dti tract stats for the fmajor_PP tract see the attached script file @tractstats2table and the file list "fmajor_file_list.txt" it produced the output file "fmajor_table.txt" (attached) in the output table all the values for the variables are the same for the 7 rows. the values are from last file in the list DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt why is this? input files have different values for the various variable Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 @tractstats2table Description: Binary data DTItracts/1069/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1167/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1191/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1248/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1252/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1267/fmajor_PP_avg23_mni_flt/pathstats.overall.txt DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt fmajor Count Volume Len_Min Len_Max Len_Avg Len_Center AD_Avg AD_Avg_Weight AD_Avg_Center RD_Avg RD_Avg_Weight RD_Avg_Center MD_Avg MD_Avg_Weight MD_Avg_Center FA_Avg FA_Avg_Weight FA_Avg_Center freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 freesurfer 1000.0 144.0 29.050.036.896 34.00.00133574 0.00136416 0.00126968 0.000659806 0.000681595 0.000547329 0.000885118 0.000909116 0.000788114 0.4350630.433158 0.486111 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tractstats@table output oddity
if i do the 7 subjects individually, 1 by 1 with the tractstats2table for each subject, the data in the table are ok, it's just when I process them all with 1 tractsstat2table command, that the data is the same in each row of the output Jon - Original Message - From: "Jon Wieser" To: "freesurfer" Sent: Wednesday, March 27, 2013 12:17:40 PM Subject: [Freesurfer] tractstats@table output oddity I ran tractstats2table to make a table of my dti tract stats for the fmajor_PP tract see the attached script file @tractstats2table and the file list "fmajor_file_list.txt" it produced the output file "fmajor_table.txt" (attached) in the output table all the values for the variables are the same for the 7 rows. the values are from last file in the list DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt why is this? input files have different values for the various variable Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error during trac-all -prep
attached is the dmrirc config file - Original Message - From: "Jon Wieser" To: "freesurfer" Sent: Wednesday, March 27, 2013 3:33:03 PM Subject: [Freesurfer] error during trac-all -prep i ran trac-all -prep -c dmrirc_single_subject and got the error : fslmaths /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask.nii.gz -mul /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/notventricles.nii.gz /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask-vent.nii.gz Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort I have attached the trac-all .log and trac-all.error files I don't know how to fix this error Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 dmrirc_single_subject Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tractstats@table output oddity
Subject: [Freesurfer] tractstats@table output oddity I ran tractstats2table to make a table of my dti tract stats for the fmajor_PP tract see the attached script file @tractstats2table and the file list "fmajor_file_list.txt" it produced the output file "fmajor_table.txt" (attached) in the output table all the values for the variables are the same for the 7 rows. the values are from last file in the list DTItracts/1276/fmajor_PP_avg23_mni_flt/pathstats.overall.txt why is this? input files have different values for the various variable Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] merging dti data
we captured some dti data. there were 2 runs. we acquired in the axial plane, 2mm slice thickness the first run captured the lower half of the brain, slice locations: I56-S20, and the second run captured the upper half of the brain S16-S92. i have made briks from each of these runs. I can convert the briks to nifti files I want to merge the nifti files together to analyze the data in tracula In the past i have merged data from two dti runs, but each run have covered the entire brain, with the following commands mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz would it work to concat the two half brain niftis into one file and analyze that with tracula? (I will concat the bvec and bvals files too) would this cause problems doing it this way? Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] merging dti data
Those commands were given to me by Anastasia. they work fine for merging two whole brain datasets. jon - Original Message - From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 10:13:05 PM Subject: Re: [Freesurfer] merging dti data Hi Jon, I don't know how to make this work, but I'm sure that those commands will not do it. Sorry:( doug On 4/10/13 1:13 PM, Jon Wieser wrote: > we captured some dti data. there were 2 runs. we acquired in the axial plane, > 2mm slice thickness the first run captured the lower half of the brain, slice > locations: I56-S20, and the second run captured the upper half of the brain > S16-S92. i have made briks from each of these runs. > I can convert the briks to nifti files > I want to merge the nifti files together to analyze the data in tracula > > In the past i have merged data from two dti runs, but each run have covered > the entire brain, with the following commands > > mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz > mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz > mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz > > > would it work to concat the two half brain niftis into one file and analyze > that with tracula? > (I will concat the bvec and bvals files too) > would this cause problems doing it this way? > Thanks > Jon > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] merging dti data
the gradients were the same for each slab. What is the difficulty with runnning the merged brain halves in tracula? I have another to do it that I am going to try. I made AFNI Brik's of the two slabs, and merged them together into one AFNI brik with the AFNI command 3dZcat. I made a nifti file from the merged afni brik. i will try running tracula on the merged nifti file. Jon - Original Message - From: "Douglas Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Thursday, April 11, 2013 9:56:53 AM Subject: Re: [Freesurfer] merging dti data yes, they work for whole brain, but not if you have two brain halves. You might be able to do something in matlab. I assume the gradient direction order was the same for both slabs? doug On 4/11/13 10:36 AM, Jon Wieser wrote: > Those commands were given to me by Anastasia. they work fine for merging two > whole brain datasets. > jon > > - Original Message - > From: "Douglas Greve" > To: freesurfer@nmr.mgh.harvard.edu > Sent: Wednesday, April 10, 2013 10:13:05 PM > Subject: Re: [Freesurfer] merging dti data > > > Hi Jon, I don't know how to make this work, but I'm sure that those > commands will not do it. Sorry:( > doug > > > > > On 4/10/13 1:13 PM, Jon Wieser wrote: >> we captured some dti data. there were 2 runs. we acquired in the axial >> plane, 2mm slice thickness the first run captured the lower half of the >> brain, slice locations: I56-S20, and the second run captured the upper half >> of the brain S16-S92. i have made briks from each of these runs. >> I can convert the briks to nifti files >> I want to merge the nifti files together to analyze the data in tracula >> >> In the past i have merged data from two dti runs, but each run have covered >> the entire brain, with the following commands >> >> mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz >> mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz >> mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz >> >> >> would it work to concat the two half brain niftis into one file and analyze >> that with tracula? >> (I will concat the bvec and bvals files too) >> would this cause problems doing it this way? >> Thanks >> Jon >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] merging dti data
Hi Doug I can motion correct the briks with 3dvolreg Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Thursday, April 11, 2013 11:22:13 AM Subject: Re: [Freesurfer] merging dti data That might work. I think "motion" correction is going to be your biggest problem since the slabs were acquired at different times. On 04/11/2013 11:05 AM, Jon Wieser wrote: > the gradients were the same for each slab. What is the difficulty with > runnning the merged brain halves in tracula? > > > I have another to do it that I am going to try. I made AFNI Brik's of the > two slabs, and merged them together into one AFNI brik with the AFNI command > 3dZcat. I made a nifti file from the merged afni brik. i will try running > tracula on the merged nifti file. > > Jon > > - Original Message - > From: "Douglas Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Thursday, April 11, 2013 9:56:53 AM > Subject: Re: [Freesurfer] merging dti data > > yes, they work for whole brain, but not if you have two brain halves. > You might be able to do something in matlab. I assume the gradient > direction order was the same for both slabs? > doug > > > > > On 4/11/13 10:36 AM, Jon Wieser wrote: >> Those commands were given to me by Anastasia. they work fine for merging >> two whole brain datasets. >> jon >> >> - Original Message - >> From: "Douglas Greve" >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Wednesday, April 10, 2013 10:13:05 PM >> Subject: Re: [Freesurfer] merging dti data >> >> >> Hi Jon, I don't know how to make this work, but I'm sure that those >> commands will not do it. Sorry:( >> doug >> >> >> >> >> On 4/10/13 1:13 PM, Jon Wieser wrote: >>> we captured some dti data. there were 2 runs. we acquired in the axial >>> plane, 2mm slice thickness the first run captured the lower half of the >>> brain, slice locations: I56-S20, and the second run captured the upper half >>> of the brain S16-S92. i have made briks from each of these runs. >>> I can convert the briks to nifti files >>> I want to merge the nifti files together to analyze the data in tracula >>> >>> In the past i have merged data from two dti runs, but each run have covered >>> the entire brain, with the following commands >>> >>> mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz >>> mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz >>> mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz >>> >>> >>> would it work to concat the two half brain niftis into one file and analyze >>> that with tracula? >>> (I will concat the bvec and bvals files too) >>> would this cause problems doing it this way? >>> Thanks >>> Jon >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] merging dti data
Hi Doug we got good results with the dit of the merged brik's Jon - Original Message - From: "Douglas N Greve" To: "Jon Wieser" Cc: "freesurfer" Sent: Thursday, April 11, 2013 11:22:13 AM Subject: Re: [Freesurfer] merging dti data That might work. I think "motion" correction is going to be your biggest problem since the slabs were acquired at different times. On 04/11/2013 11:05 AM, Jon Wieser wrote: > the gradients were the same for each slab. What is the difficulty with > runnning the merged brain halves in tracula? > > > I have another to do it that I am going to try. I made AFNI Brik's of the > two slabs, and merged them together into one AFNI brik with the AFNI command > 3dZcat. I made a nifti file from the merged afni brik. i will try running > tracula on the merged nifti file. > > Jon > > - Original Message - > From: "Douglas Greve" > To: "Jon Wieser" > Cc: "freesurfer" > Sent: Thursday, April 11, 2013 9:56:53 AM > Subject: Re: [Freesurfer] merging dti data > > yes, they work for whole brain, but not if you have two brain halves. > You might be able to do something in matlab. I assume the gradient > direction order was the same for both slabs? > doug > > > > > On 4/11/13 10:36 AM, Jon Wieser wrote: >> Those commands were given to me by Anastasia. they work fine for merging >> two whole brain datasets. >> jon >> >> - Original Message - >> From: "Douglas Greve" >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Wednesday, April 10, 2013 10:13:05 PM >> Subject: Re: [Freesurfer] merging dti data >> >> >> Hi Jon, I don't know how to make this work, but I'm sure that those >> commands will not do it. Sorry:( >> doug >> >> >> >> >> On 4/10/13 1:13 PM, Jon Wieser wrote: >>> we captured some dti data. there were 2 runs. we acquired in the axial >>> plane, 2mm slice thickness the first run captured the lower half of the >>> brain, slice locations: I56-S20, and the second run captured the upper half >>> of the brain S16-S92. i have made briks from each of these runs. >>> I can convert the briks to nifti files >>> I want to merge the nifti files together to analyze the data in tracula >>> >>> In the past i have merged data from two dti runs, but each run have covered >>> the entire brain, with the following commands >>> >>> mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz >>> mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz >>> mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz >>> >>> >>> would it work to concat the two half brain niftis into one file and analyze >>> that with tracula? >>> (I will concat the bvec and bvals files too) >>> would this cause problems doing it this way? >>> Thanks >>> Jon >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] convert phillips PAr/Rec files
dear FS experts I have some PAR/REc format anatomical file from a Phillips scanner. I want to convert the to nifti or MGZ format for freesurfer. how do I do this conversion what program do I use? Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Qdec and GLM ROI analysis
I am interested ing doing a group surfaces analysis like that specified in: ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis, or http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28cortical%29%7C%28thickness%29 but I want to limit the analysis to a specific ROI. how do i do this? -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Restricting ROI Analysis
it there a way to mask the data before running the Qdec analysis on it? - Original Message - From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Sent: Sunday, May 12, 2013 11:24:12 PM Subject: Re: [Freesurfer] Restricting ROI Analysis Hi Skyler, I don't think we have the ability to restrict the analysis to an ROI in QDEC. You can do it with mri_glmfit with the --mask or --label option. doug On 5/12/13 4:25 PM, Skyler Gabriel Shollenbarger wrote: > Hi everyone, > > We are trying to restrict an analysis using Qdec to a region of interest. We > have successfully created the ROI mask, however the analysis continues to be > run on the entire brain. Any help is greatly appreciated. > > Thanks, > Skyler and Jon > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkmedit on ssh remote machine error
hi freesurfer folks I'm ssh'ing to from one MAc to another X11 is on both machines MAC OS X 10.6.8 When I start TKmedit with: (freesurfer files are in the freesurfer directory) tkmedit freesurfer brainmask.mgz -aux T1.mgz I get the errors: Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] : kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] : kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] : kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] : unknown error code: invalid drawable error: xp_attach_gl_context returned: 2 tkmedit GUI opens and the image window opens, but the image window is blank (white) , (no image of the brain) i have set X11forwarding to yes in the /etc/sshd_config file so xeyes works ok remotely Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tkmedit on ssh remote machine error
both machines have Mac OS X 10.6.8 the tkmedit works fine when not logged in remotely there is no error and the brain image is there Jon - Original Message - From: "Z K" To: "Jon Wieser" Cc: "freesurfer" Sent: Thursday, May 30, 2013 12:16:55 PM Subject: Re: [Freesurfer] tkmedit on ssh remote machine error Jon, I have not seen or heard of this error before... are both machines Mac OSX 10.6.8? Also, will the same command will produce a brain image when not logged in remotely? -Zeke On 05/30/2013 12:43 PM, Jon Wieser wrote: > > hi freesurfer folks > > I'm ssh'ing to from one MAc to another > X11 is on both machines > MAC OS X 10.6.8 > > When I start TKmedit with: (freesurfer files are in the freesurfer directory) > > tkmedit freesurfer brainmask.mgz -aux T1.mgz > > > I get the errors: > Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] : > kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 349 > Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] : > kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as > they are logged. > Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] : > kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0x15d > Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[78500] : unknown > error code: invalid drawable > error: xp_attach_gl_context returned: 2 > > > > tkmedit GUI opens and the image window opens, but the image window is > blank (white) , (no image of the brain) > > > > > i have set X11forwarding to yes in the /etc/sshd_config file > so xeyes works ok remotely > Jon > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit on ssh remote machine error
yes, I have ForwardX11Trusted yes in ssh_config and I do ssh -Y Jon - Original Message - From: "R Edgar" To: "Jon Wieser" Cc: "Z K" , "freesurfer" Sent: Thursday, May 30, 2013 3:26:05 PM Subject: Re: [Freesurfer] tkmedit on ssh remote machine error On Thu, May 30, 2013 at 2:37 PM, Jon Wieser wrote: > both machines have Mac OS X 10.6.8 > > the tkmedit works fine when not logged in remotely > there is no error and the brain image is there Did you do "ssh -Y" or have "ForwardX11Trusted yes" in your ssh.config? Richard -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] trac-all problem
fer/dmri/dwi_tmp0033 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053 processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054 mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0 Usage: fslroi fslroi fslroi Note: indexing (in both time and space) starts with 0 not 1! Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013 can you tell me how to fix this? Thanks Jon Wieser UW-Milwaukee dmrirc_single_subject Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] running freesurfer on multi core machine
Hi, I am runnning fressurfer on a Mac with 23.06 Ghz 6-core intel Xeon processors. is it possible to run recon-all and trac-all on multiple cores. Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: trac-all problem
ation: /Studies/MJMRI/MJ0012/freesurfer/dmri/xfms/diff2mni.flt.mat Number of burn-in samples: 200 Number of post-burn-in samples: 5000 Keep every: 5-th sample Update proposal every: 0-th sample Loading spline control points from /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lh.cst_AS_avg23_mni_flt_cpts_5.txt Loading spline mask from /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Creating output directory /Studies/MJMRI/MJ0012/freesurfer/dpath/5cpts/priormni/seg14/initmni/regflt/lh.cst_AS_avg23_mni_flt Loading DWIs from /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz Loading mask from /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Studies/MJMRI/MJ0012/freesurfer/dmri.bedpostX dmri_paths(38479) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 60): could not allocate 262144 bytes for 1193th slice Cannot allocate memory Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-paths exited with ERRORS at Mon Feb 18 09:14:48 CST 2013 how can I fix this? Jon - Original Message - From: "Anastasia Yendiki" To: "Jon Wieser" Sent: Thursday, February 14, 2013 1:22:02 PM Subject: Re: [Freesurfer] trac-all problem Great! On Thu, 14 Feb 2013, Jon Wieser wrote: > Hi Anastasia, > > update on my processing. > I finished recon-all -autorecon1 ,-autorecon2, and -autorecon3 . > I finished trac -prep with No errors! > moving on the Trac-all -bedp > > > thanks! > Jon > > > - Original Message - > From: "Anastasia Yendiki" > To: "Jon Wieser" > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, February 12, 2013 3:44:59 PM > Subject: Re: [Freesurfer] trac-all problem > > > Hi Jon - You'll the aparc+aseg.mgz (cortical parcellation + subcortical > segmentation). The basis of TRACULA is that it uses the underlying anatomy > to reconstruct the tracts. > > a.y > > On Tue, 12 Feb 2013, Jon Wieser wrote: > >> no i have not run recon-all yet on this dataset, >> do i need to run recon-all with -autorecon1 ,-autorecon2, and -autorecon3 >> before i analyze the dti data? >> >> thanks >> Jon >> >> - Original Message - >> From: "Anastasia Yendiki" >> To: "Jon Wieser" >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Tuesday, February 12, 2013 3:34:19 PM >> Subject: Re: [Freesurfer] trac-all problem >> >> >> Hi Jon - Have you run freesurfer (recon-all) on your T1 data? >> >> a.y >> >> On Tue, 12 Feb 2013, Jon Wieser wrote: >> >>> i got past the problem with the bvesc, and bvals, >>> >>> >>> my current output has a new problem: >>> here's the last part of the output. >>> >>> >>> >>> #@# Tensor fit Tue Feb 12 15:24:51 CST 2013 >>> dtifit -k /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz -m >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -r >>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs -b >>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals -o >>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dtifit >>> 0 256 0 256 0 60 >>> 0 slices processed >>> 1 slices processed >>> 2 slices processed >>> 3 slices processed >>> 4 slices processed >>> 5 slices processed >>> 6 slices processed >>> 7 slices processed >>> 8 slices processed >>> 9 slices processed >>> 10 slices processed >>> 11 slices processed >>> 12 slices processed >>> 13 slices processed >>> 14 slices processed >>> 15 slices processed >>> 16 slices processed >>> 17 slices processed >>> 18 slices processed >>> 19 slices processed >>> 20 slices processed >>> 21 slices processed >>> 22 slices processed >>> 23 slices processed >>> 24 slices processed >>> 25 slices processed >>> 26 slices processed >>> 27 slices processed >>> 28 slices processed >>> 29 slices processed >>> 30 slices processed >>> 31 slices processed >>> 32 slices processed >>> 33 slices processed >>> 34 slices processed >>> 35 slices processed >>> 36 slices processed >>> 37 slices processed >>> 38 slices processed >>> 39 slices processed >>> 40 slices processed >>> 41 slices processed &
[Freesurfer] problem with trac-all -prep proc stage
hello i ran a trac-all -prep -c ./dmrirc_single_subject and got the following error: flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2anat.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.flt.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2anat.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/diff2mni.bbr.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2anat.mat convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/mni2anatorig.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/anatorig2mni.mat ln -sfn /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/cvs/cvs_avg35 /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs mri_cvs_register --mov freesurfer --template cvs_avg35 --outdir /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs Log file is freesurfer_to_cvs_avg35.mri_cvs_register.1302261152.log Tue Feb 26 11:52:22 CST 2013 --mov freesurfer --template cvs_avg35 --outdir /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs $Id: mri_cvs_register,v 1.4.2.2 2010/08/11 17:52:00 nicks Exp $ cerebrum.uits.uwm.edu Darwin cerebrum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 The outdir: /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs mris_resample --atlas_reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/cvs_avg35/surf/lh.sphere --annot /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/label/lh.aparc.annot /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs/lh.resample.aparc.annot --subject_surf /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/surf/lh.white --subject_reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191/freesurfer/surf/lh.cvs.tocvs_avg35.sphere.reg --out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1191//freesurfer/dmri/xfms/cvs/lh.resample.white Exception caught while parsing cmd-line ambiguous option annot Darwin cerebrum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 trac-preproc exited with ERRORS at Tue Feb 26 11:52:22 CST 2013 Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] processing 2 dti's from 1 experiment
hello, we have acquired dti scans on a subject during a FMRI experiment. is it possible to process both dti's with tracule to get an average of the 2 dti's? If so, how do I setup the config file for this? Thanks Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer
Hi Nicole, It looks like recon-all -autorecon2 had trouble segmenting the gray/white matter. you can try using 3duniformize to make the gray,white matter more uniform, before doing the freesurfes recon-all. you can also try skullstrippong in afni with 3dskullstrip first, before freesurfer processing. I have attached script files for the uniformize and skullstrip. if this does not fix it, I can come to help you, or you can e-mail the problem to the freesurfer people at freesurfer@nmr.mgh.harvard.edu . They are very helpful and will response relatively quickly. Jon - Original Message - From: "Nicole T Nowak-Saenz" To: "Jon Alan Wieser" Sent: Thursday, March 7, 2013 12:35:57 PM Subject: Freesurfer Hi Jon, I think you mentioned working with Freesurfer. Have you ever seen anything like this? I'm hoping the problems with segmentation, and white/pial lines are due to the recon-all somehow leaving out half the brain (e.g., temporal lobes). To me it looks like half the brain is missing, yet some skull remains. I have a feeling this will require more than adjusting a watershed parameter. Any clue how these errors occured or what to do about them? I should mention I had to use a flag which was provided in the failed recon-all log to correct an error like this one: DICOM WARNING: file 00020002.dcm has Rescale tags. If this is something you know something about and have a few minutes to address, I would appreciate it. If not, I completely understand. Nicole @skullstrip Description: Binary data @uniformize Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] LGI
i am trying to computer the LGI local gyrification index with freesurfer. I have Matlab on my machine. I got the following error: recon-all -s freesurfer -localGI Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 wieser admin 506264 Mar 18 12:37 /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 /Studies/MJMRI/MJ0012/freesurfer/surf # #@# Local Gyrification Index lh Mon Mar 18 12:43:04 CDT 2013 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin psy-cerebellum.wifi.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 recon-all -s freesurfer exited with ERRORS at Mon Mar 18 12:43:04 CDT 2013 For more details, see the log file /Studies/MJMRI/MJ0012/freesurfer/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting JOn -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] LGI qdec analysis on longitiudinal data
Hi freesurfer experts I am trying to analyze the longitudinal effects on LGI. I've run all my subject's through the longitudinal processing stream. I set-up my qdec dat file: fsidfsid-base years 100674-0107 100674_base 1.6 100674-0408 100674_base 2.8 100674-0605 100674_base 0 100712-0505 100712_base 0 100712-0708 100712_base 3.2 100712-1006 100712_base 1.4 100724-0605 100724_base 0 100724-0808 100724_base 3.2 100724-1206 100724_base 1.5 100733-0106 100733_base 0 100733-0507 100733_base 1.3 100733-1008 100733_base 2.8 I ran long_mris_slopse for both hemispheres: long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc i also ran long_qdec_table long_qdec_table --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --cross --out ./qdec/cross.qdec.table.dat then I ran qdec: qdec --table ./qdec/cross.qdec.table.dat I specified pial_lgi as the Measure, and selected years as the covariate when I press Analyze, I get the following error: Error in Analyze: Couldn't open 100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgz or mgh file when looking in the directories, I have lh.pial_lgi.fwhm10.fsaverage.mgh files in the 100674-0107.long.100674_base directories: \100674-0107.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0107.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh but not in the following directories 100674_base/surf 100712_base/surf 100724_base/surf 100733_base/surf How can I fix this? Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: LGI qdec analysis on longitiudinal data
I added the following lines to the .Qdecrc file in my home directory MEASURE1 = long.pial_lgi-avg MEASURE2 = long.pial_lgi-rate MEASURE3 = long.pial_lgi-pc1 MEASURE4 = long.pial_lgi-spc qdec's Analyze is working now. what specifically do :( long.pial_lgi-avg, long.pial_lgi-rate, long.pial_lgi-pc1, long.pial_lgi-spc ) measure regarding the LGI ? Jon - Forwarded Message - From: "Jon Wieser" To: "freesurfer" Sent: Monday, May 19, 2014 2:53:43 PM Subject: [Freesurfer] LGI qdec analysis on longitiudinal data Hi freesurfer experts I am trying to analyze the longitudinal effects on LGI. I've run all my subject's through the longitudinal processing stream. I set-up my qdec dat file: fsidfsid-base years 100674-0107 100674_base 1.6 100674-0408 100674_base 2.8 100674-0605 100674_base 0 100712-0505 100712_base 0 100712-0708 100712_base 3.2 100712-1006 100712_base 1.4 100724-0605 100724_base 0 100724-0808 100724_base 3.2 100724-1206 100724_base 1.5 100733-0106 100733_base 0 100733-0507 100733_base 1.3 100733-1008 100733_base 2.8 I ran long_mris_slopse for both hemispheres: long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc i also ran long_qdec_table long_qdec_table --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --cross --out ./qdec/cross.qdec.table.dat then I ran qdec: qdec --table ./qdec/cross.qdec.table.dat I specified pial_lgi as the Measure, and selected years as the covariate when I press Analyze, I get the following error: Error in Analyze: Couldn't open 100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgz or mgh file when looking in the directories, I have lh.pial_lgi.fwhm10.fsaverage.mgh files in the 100674-0107.long.100674_base directories: \100674-0107.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0107.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh but not in the following directories 100674_base/surf 100712_base/surf 100724_base/surf 100733_base/surf How can I fix this? Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: LGI qdec analysis on longitiudinal data
Thanks, Martin for the info. We are studying the effect of drug usage on LGI over time Jon - Original Message - From: "Martin Reuter" To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 19, 2014 3:30:48 PM Subject: Re: [Freesurfer] Fwd: LGI qdec analysis on longitiudinal data Just saw that you already found those settings. these measures are the vertex wise results from the first level analysis on the (smoothed) LGI data. avg: average lgi at that location across time (within each subject). rate: the change of lgi per time unit (years). pc1: the percent change with respect to the first time point spc: symmetrized percent change (rate with respect to the average) if any of this is meaningful for LGI, I don't know, you were the one trying to do this analysis ;-). Best, Martin On 05/19/2014 04:20 PM, Jon Wieser wrote: > I added the following lines to the .Qdecrc file in my home directory > > MEASURE1 = long.pial_lgi-avg > MEASURE2 = long.pial_lgi-rate > MEASURE3 = long.pial_lgi-pc1 > MEASURE4 = long.pial_lgi-spc > > > qdec's Analyze is working now. > > what specifically do :( long.pial_lgi-avg, long.pial_lgi-rate, > long.pial_lgi-pc1, long.pial_lgi-spc ) measure regarding the LGI ? > > > Jon > > - Forwarded Message - > From: "Jon Wieser" > To: "freesurfer" > Sent: Monday, May 19, 2014 2:53:43 PM > Subject: [Freesurfer] LGI qdec analysis on longitiudinal data > > Hi freesurfer experts > > I am trying to analyze the longitudinal effects on LGI. I've run all my > subject's through the longitudinal processing stream. > > I set-up my qdec dat file: > > fsid fsid-base years > 100674-0107 100674_base 1.6 > 100674-0408 100674_base 2.8 > 100674-0605 100674_base 0 > 100712-0505 100712_base 0 > 100712-0708 100712_base 3.2 > 100712-1006 100712_base 1.4 > 100724-0605 100724_base 0 > 100724-0808 100724_base 3.2 > 100724-1206 100724_base 1.5 > 100733-0106 100733_base 0 > 100733-0507 100733_base 1.3 > 100733-1008 100733_base 2.8 > > I ran long_mris_slopse for both hemispheres: > > long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi > lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years > --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc > > long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi > rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years > --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc > > i also ran long_qdec_table > > long_qdec_table --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --cross --out > ./qdec/cross.qdec.table.dat > > > then I ran qdec: > > qdec --table ./qdec/cross.qdec.table.dat > > I specified pial_lgi as the Measure, and selected years as the covariate > when I press Analyze, I get the following error: > Error in Analyze: Couldn't open > 100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgz or mgh file > > > > when looking in the directories, I have lh.pial_lgi.fwhm10.fsaverage.mgh > files in the 100674-0107.long.100674_base directories: > > \100674-0107.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100724-0605.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100674-0107.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100724-0605.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100674-0408.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100724-0808.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100674-0408.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100724-0808.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100674-0605.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100724-1206.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100674-0605.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100724-1206.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100712-0505.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100733-0106.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100712-0505.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100733-0106.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100712-0708.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100733-0507.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh > 100712-0708.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100733-0507.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh > 100712-1006.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh
[Freesurfer] ERROR: dimension mismatch between input volume and seg
hi freesurfer experts I am compiling the FA segment stats for several subject I used mri_vol2vol --mov fa.nii --reg register.dat --fstarg ../mri/orig.mgz --interp nearest --o fa.anat.mgh then I used: mri_segstats --seg mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stats for some of my subjects, Iam getting the following error: mri_segstats --seg mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --i dti/fa.anat.mgh --sum dti/fa.stat sysname Darwin hostname psy-blackbird.ad.uwm.edu machine x86_64 user wieser UseRobust 0 Loading mri/wmparc.mgz Loading dti/fa.anat.mgh ERROR: dimension mismatch between input volume and seg input 256 256 192 seg 256 256 256 can you tell me how to fix this? thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
