Re: [Freesurfer] bring volumes to fsaverage space
Dear Lilla and freesurfers, I hvae tried to rub the mri_CVS_register and got the following error: VolumeMorph load - failed to open input stream. I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Any idea how to fix this> Log file atttached Thanks! Shani On Fri, Oct 30, 2015 at 11:17 PM, Lilla Zollei wrote: > > Hi Shani, > > Sure. You can do > > mri_cvs_register --help > > and that should give you lots of information. > > Alternatively you can also go to > https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register > > and read through the presentation that we give at the FS course: > http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt > > Best, Lilla > > > On Fri, 30 Oct 2015, Shani Ben Amitay wrote: > > >> Hello >> Can you please direct me to more information about the CVS. >> Thanks! >> Shani >> >> בתאריך 30 באוק' 2015 14:39, "Bruce Fischl" >> כתב: >> Hi Shani >> >> you can use mri_vol2vol with the talairach.m3z. Alternatively, you >> can run CVS which will give you more accurate cortical matching and use the >> transform that it produces. >> >> cheers >> Bruce >> On Fri, 30 Oct 2015, Shani Ben Amitay wrote: >> >> Dear freesurfers, >> I would like to know what will be the best way to bring >> volumes in the >> individual subject's space to the fsaverage space. >> >> Thanks, >> Shani >> >> >> ___ >> 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 > > > 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. > > Logfile for mri_cvs_register Sun Nov 1 22:32:09 EET 2015 --mov RETU $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ yaniva17 Linux yaniva17 3.2.0-90-generic #128-Ubuntu SMP Fri Aug 14 21:43:58 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux asegfname aseg Using m3z type morph files. mri_cvs_register: Step 1 (spherical registration) took 0 seconds surf2vol -fixed_mri /usr/local/freesurfer/subjects//cvs_avg35/mri//norm.mgz -moving_mri /media/drivee/subjects/RETU/mri//norm.mgz -fixed_surf /usr/local/freesurfer/subjects//cvs_avg35/surf//lh.white -moving_surf /media/drivee/subjects/RETU/cvs/lh.resample.white -fixed_surf_2 /usr/local/freesurfer/subjects//cvs_avg35/surf//rh.white -moving_surf_2 /media/drivee/subjects/RETU/cvs/rh.resample.white -fixed_surf_3 /usr/local/freesurfer/subjects//cvs_avg35/surf//lh.pial -moving_surf_3 /media/drivee/subjects/RETU/cvs/lh.resample.pial -fixed_surf_4 /usr/local/freesurfer/subjects//cvs_avg35/surf//rh.pial -moving_surf_4 /media/drivee/subjects/RETU/cvs/rh.resample.pial -aparc /usr/local/freesurfer/subjects//cvs_avg35/label//lh.aparc.annot -aparc_2 /usr/local/freesurfer/subjects//cvs_avg35/label//rh.aparc.annot -aparc_3 /usr/local/freesurfer/subjects//cvs_avg35/label//lh.aparc.annot -aparc_4 /usr/local/freesurfer/subjects//cvs_avg35/label//rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -penalty_weight 1000 -fem_steps 17 -elt_vol_range 5.0,10.0 -topology_old -compress -pc_type jacobi -ksp_type preonly -ksp_view -ksp_converged_reason -poisson .3 -young 1000 -cache_transform /media/drivee/subjects/RETU/cvs/transform.txt -out /media/drivee/subjects/RETU/cvs/el_reg_tocvs_avg35.mgz -out_mesh /media/drivee/subjects/RETU/cvs/el_reg_tocvs_avg35 -out_affine /media/drivee/subjects/RETU/cvs/el_reg_tocvs_avg35.affine.mgz No ASEG option present No field output option specified will use default value out_field.mgz will cache transform in file /media/drivee/subjects/RETU/cvs/transform.txt reading fixed volume reading moving volume surface name = /usr/local/freesurfer/subjects//cvs_avg35/surf//lh.white type = 0 surface name = /usr/local/freesurfer/subjects//cvs_avg35/surf//rh.white type = 0 surface name = /usr/local/freesurfer/subjects//cvs_avg35/surf//lh.pial type = 1 surf
[Freesurfer] Timepoints and Analysis
Dear FreeSurfer group, I have a question regarding timepoints and analysis. For example, lets say we have a data-set of 80 subjects with the following timepoints: baseline, 6 weeks, 6 months, 1 year and 2 years follow-up. Two different studies on the same data needs to be performed. a) Study_1 with two timepoints (baseline and 6 weeks) b) Study_2 with all time timepoints (baseline, 6 weeks, 6 months, 1 year and 2 years follow-up). As i understand, the more time points the better the [BASE] you will get. The BASE is going to be edited Therefore, even though Study_1 only is going to be using two timepoints, do you still recommend to include all the 5 time points in creating the [BASE] even though only 2 time points will be used? Best regards, Kasper Jessen ___ 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] Timepoints and Analysis
Hi Kasper, generally the answer is yes, include all time point in the base, qc/edit and do whatever analysis you want on the final .long.base directories. This will guarantee a few nice things: 1. you will only need to do 1 pass through with QC and editing 2. information from other time points can help cleanup results for earlier time points (e.g. if 6 month image has motion, including year 1 and year 2 can help clean up surfaces there). 3. You have 1 consistent set of measurements, independent of what time points will actually be analyzed. These argument usually overweight the disadvantages: 1. You need to wait until all data is there (in your case no disadvantage) 2. The longer you wait (in time) the further the base will move away from the initial time points. This is a disadvantage in your case, as 2 years could have some significant atrophy, and if you are only interested in test retest or 6 weeks (which is basically test-retest, unless you do some amazing magic there), you may be better off to run the test-retest component separately, to avoid getting an influence from future real atrophy cases. Usually this influence is limited in my tests, but no thorough analysis has been done on this yet. So it depends on your study, on what you expect to happen, on you time for QC and editing (so also on your sample size). Etc. Also if you are looking for real effects in only 6 weeks, make sure you especially avoid/control biases such as hydration levels, or different motion levels, which could produce spurious effects: hydration: http://www.ajnr.org/content/early/2015/09/17/ajnr.A4508 Head motion: http://www.sciencedirect.com/science/article/pii/S1053811914009975 Cheers, Martin On 11/02/2015 04:44 AM, Kasper Jessen wrote: Dear FreeSurfer group, I have a question regarding timepoints and analysis. For example, lets say we have a data-set of 80 subjects with the following timepoints: baseline, 6 weeks, 6 months, 1 year and 2 years follow-up. Two different studies on the same data needs to be performed. a) Study_1 with two timepoints (baseline and 6 weeks) b) Study_2 with all time timepoints (baseline, 6 weeks, 6 months, 1 year and 2 years follow-up). As i understand, the more time points the better the [BASE] you will get. The BASE is going to be edited Therefore, even though Study_1 only is going to be using two timepoints, do you still recommend to include all the 5 time points in creating the [BASE] even though only 2 time points will be used? Best regards, Kasper Jessen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu ___ 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] wrong segmentation
I used freesurfer v5.3. We have about 5 subjects that had this kind of error. We tried to fix on the wm and the result seemed good but we have no clue to deal with the aseg. Here is the link to my subject directory (no fix). http://www.mediafire.com/download/xm2igrdo33mdgmm/NCP140575_1_recon.rar Thank you and Have a nice day! Trinh 2015-10-30 23:27 GMT+07:00 Bruce Fischl : > what version are you using? I think this won't happen in V6,but if you > upload the subject dir I can check for you. To fix it check and correct the > wm.mgz and the aseg.mgz in that region > > cheers > Bruce > > On Thu, 29 Oct 2015, Thục Trinh wrote: > > Hi Freesurfer experts, >> I ran recon-all for our subjects and there is a problem with the wrong >> segmentation between the white/gray matter. this error appears in couples >> continued slices. Picture are attached. >> Do you have any suggestion to fix this error. >> >> Thank you, >> Trinh >> >> > ___ > 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 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] Differences in the asc and FreeSurfer format of the surface data
Hi Ray the ascii format is pretty barebones and doesn't have e.g. ras2vox info that freeview uses to display the surfaces properly. It's for ease of conversion and such. cheers Bruce On Mon, 2 Nov 2015, Razlighi, Qolamreza R. wrote: > Hi Guys, > Why converting a surface to .asc format changes its spatial orientation? > Specifically, I have converted lh.while to lh.white.asc (using: mris_convert > lh.white lh.white.asc) and plot both of them using freeview but they are not > corresponding. In fact, lh.white corresponds to the volume image (e.g > orig.mgz) but the lh.white.asc doesn't. See the attached screenshot. The red > curve is the lh.white.asc. > Any explanation would be greatly appreciated. > > Best > > ___ 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] Hippocampal Subfields 6.0 with 5.3 recons
Hello all, I was wondering if anyone with knowledge of the new hippocampal subfield segmentation that is going to be released with version 6.0 could answer a quick question. We have previously processed subjects in v5.3 and would like to use the new hippocampal seg algorithm. How "standalone" is the new process? Does the new process use any inputs from the recon-all stream which have changed in the upcoming version? Thanks! -Andrew ___ 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] (no subject)
Dear all, I am very new to using TRACULA and Freesurfer. I am trying to apply tracula on the provided tutorial data. When I ran the command trac-all -prep -c dmrirc.tutorial, after eddy current correction, I get this error: -- D. ___ 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] Tracula ends with errors
Dear all, I am very new to using TRACULA and Freesurfer. I am trying to apply tracula on the provided tutorial data. When I ran the command trac-all -prep -c dmrirc.tutorial, after eddy current correction, I get this error: mv -f /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs.norot xfmrot /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.ecclog /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs.norot /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. n -sf /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/data.nii.gz mri_convert --frame 0 /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999278, -0.0375823, -0.00564044) j_ras = (-0.0367492, 0.917788, 0.395367) k_ras = (0.00968205, -0.395289, 0.918506) keeping frame 0 writing to /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz... mri_concat --i /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz --mean --o /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz bet /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain_mask.nii.gz /data_augus t/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff #- #@# Inter-subject registration Mon Nov 2 15:39:02 CET 2015 flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain.nii.gz -ref /data_RAID/Kathrin/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain_mni.nii.gz -omat /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.mat -cost corratio convert_xfm -omat /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/mni2diff.mat -inverse /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.mat #- #@# Masks Mon Nov 2 15:39:20 CET 2015 flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/lowb_brain_mask.nii.gz -ref /data_RAID/Kathrin/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/lowb_brain_mask.nii.gz -ref /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/brain_anat_orig.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/nodif_brain_mask.nii.gz #- #@# Tensor fit Mon Nov 2 15:39:23 CET 2015 dtifit -k /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz -m /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs -b /data_august/Deniz/tutorial/tutorial_data/diffusion_t
[Freesurfer] Mac Version and Output differs
Dear FreeSurfer group, I have tested the data output on the same subjects using the same FreeSurfer version but on different machines, a MacPro and a iMac. The output are different, which argues that it is important to run freesurfer on the same computer on all your subjects. Is it due to a randomisation in freesurfer (maybe because of seed points)? Is it possible to get the same results even though you run in on different computers? *MacPro:* build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin mac-pro-2014.regionh.top.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 *iMac: * build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Nikolajs-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 Best regards, Kasper Jessen ___ 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] Mac Version and Output differs
Dear Kasper, This is due to the different operating systems you are running not differences in the computers. Your iMac is running ~10.7 and your MacPro is running ~10.9. You should always run your analysis on the same operating system, however you should get no differences on different computers with the same operating system. hth d On Mon, Nov 2, 2015 at 11:47 AM, Kasper Jessen wrote: > Dear FreeSurfer group, > > I have tested the data output on the same subjects using the same FreeSurfer > version but on different machines, a MacPro and a iMac. The output are > different, which argues that it is important to run freesurfer on the same > computer on all your subjects. > > Is it due to a randomisation in freesurfer (maybe because of seed points)? > Is it possible to get the same results even though you run in on different > computers? > > MacPro: > build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 > Darwin mac-pro-2014.regionh.top.local 13.4.0 Darwin Kernel Version 13.4.0: > Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 > > iMac: > build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 > Darwin Nikolajs-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 > 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 > > Best regards, > Kasper Jessen > > ___ > 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] Fw: recon-all crashing
Can you try this version? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.mac If that fails, can you send me your dicoms through our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2 doug On 11/02/2015 11:14 AM, Biekman, Brian Darnell wrote: > > > > > > *From:* Biekman, Brian Darnell > *Sent:* Wednesday, October 21, 2015 10:29 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* recon-all crashing > To Whom It May Concern: > > I am conducting FreeSurfer analysis for a multi-site project and > I'm unable to run recon-all on the T1 data for all but one of the > sites. The problem I'm dealing with is identical for all of the > subjects for which recon-all crashes. I do not want to speculate as to > why recon-all works for one of the sites but it's worth mentioning > that that site has a slightly different T1 protocol and that these > images were uploaded via a physical backup disk while for the other > sites, I downloaded the T1 data for the other sites from a database > shared by all of the project investigators. I would like to upload the > images for one the T1-weighted sequences that crashes recon-all. If > somebody could let me know how to go about that, I would really > appreciate it. Thank you. > > Here is the requested information for anyone reporting a bug: > > FREESURFER_HOME: /Applications/freesurfer > > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > > Kernel info: Darwin 15.0.0 x86_64 > > > Subject Name: 14-140-0052 > > > Command Line Executed: recon-all -all -i > /users/brianbiekman/Desktop/Brain_Scope/14-140-0052/1.dcm -s > 14-140-0052 > > > Error message generated: Screenshot of error message attached > > > recon-all log: Attached > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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] Monte Carlo in mri_glmfit-sim
Hi experts, I am having trouble performing a Monte Carlo correction using mri_glmfit-sim. My data were sampled to fsaverage and smoothed at fwhm 5, using mris_preproc. I then ran mri_glmfit on the data. I want to do my analysis/correction only in auditory cortex (AC) so I did my own simulation in AC of each hemisphere using mri_mcsim (as per http://freesurfer.net/fswiki/BuildYourOwnMonteCarlo). So far, so good. But when I try to run: mri_glmfit-sim --glmdir [my data dir]/cope7ACroi_rh.osgm.rfx/osgm --cache-label AC --grf 4 neg --cwpvalthresh 0.05 --2space I get "fwhm: Undefined variable." I tried adding --fwhm-override 5, but it didn't help. Any thoughts? Also, can you clarify which comparison neg vs pos will give me? Thank you, Susan McLaughlin, PhD Research Scientist Laboratory for Auditory Brain Sciences & Neuroengineering Institute for Learning & Brain Sciences (I-LABS) Portage Bay Bldg. Room 204 University of Washington, Box 357988 Seattle, WA 98195-7988 Ph: (206) 616-0102 Fx: (206) 221-6472 Cell: 206-850-8638 E-mail: s...@uw.edu ___ 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] stat/math tools for MGH file
Dear FreeSurfer experts, I have a number of *.cluster.mgh files and I would like to calculate their difference and peak coordinate etc like in fslmaths or fslstats in FSL. For example, given two images, I want to know the brain regions in image1 but not in image2. Could you please recommend the general command line tools I can use for these purposes? Many thanks, Daniel ___ 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] stat/math tools for MGH file
Hi Daniel you can always convert to nifti via: mri_convert cluster.mgh cluster.nii and you will be able to use the FSL tools cheers Bruce On Tue, 3 Nov 2015, Yang, Daniel wrote: > Dear FreeSurfer experts, > > I have a number of *.cluster.mgh files and I would like to calculate their > difference and peak coordinate etc like in fslmaths or fslstats in FSL. > > For example, given two images, I want to know the brain regions in image1 > but not in image2. > > Could you please recommend the general command line tools I can use for > these purposes? > > Many thanks, > Daniel > > > > ___ 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] stat/math tools for MGH file
Hi Bruce, Yes, that’s perfect! Thanks for the reply!! :) Best, Daniel On 11/2/15, 8:48 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: >Hi Daniel > >you can always convert to nifti via: > >mri_convert cluster.mgh cluster.nii > >and you will be able to use the FSL tools > >cheers >Bruce > > >On Tue, 3 Nov 2015, Yang, Daniel >wrote: > >> Dear FreeSurfer experts, >> >> I have a number of *.cluster.mgh files and I would like to calculate >>their >> difference and peak coordinate etc like in fslmaths or fslstats in FSL. >> >> For example, given two images, I want to know the brain regions in >>image1 >> but not in image2. >> >> Could you please recommend the general command line tools I can use for >> these purposes? >> >> Many thanks, >> Daniel >> >> >> >> >___ >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 >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline&d=AwIBAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY&m=xYv-TPUIzaxdOU0_l0VVahSrl6jSBd6Rbsb4dfB0Jak&s=uRT7WmDS-H >I2mX7rEaBPdsfzQTjJgPVdORtlxQzhgvw&e= . 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/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.
