[Freesurfer] QA Tools Snaps Scrambled
Hi- I've come across a peculiar behavior with recon_checker, and am hoping someone can shed some light on this. I have used it 100's of times in the past, but not for about 2 months. I recently processed a large set of cases I wanted to QC. When I ran it, some, but not all, of the snaps were corrupted. Specifically the talairach, aseg, surfs, and all the 'detailed snaps', which are basically additional instances of the aforementioned types. The inflated, curv, and parc are all just fine. As the process runs, all images are being displayed in the pop-up windows, and the html page is created. While there have been no system changes which should affect this, I upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The problem remains. And the problem remains w/ or w/o the flag for detailed snaps. If all of the images were corrupted, I would have certainly concluded something has gone awry with my system. The fact that only some of the images are corrupted makes me scratch my head. Thoughts? Suggestions? Thanks, Wil ___ 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 preprocessing step error
Dear Freesurfer experts, I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this. Selection from log: mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz mri_convert /Users/Desktop/Tracula/diffusion_DTI/ /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/Desktop/Tracula/diffusion_DTI/... Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 Please let me know if this is not enough information. Thank you for your help. Allison ___ 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] Tracula preprocessing step error
Hi Allison - The mri_convert command at the top of your log file is trying to convert the directory /Users/Desktop/Tracula/diffusion_DTI to a nifti file. From the name of that nifti file, it looks like it's expecting to find a field map and not finding it. Hope this helps, a.y On Tue, 8 Jan 2013, Allison Gruber wrote: > Dear Freesurfer experts, > > I have encountered the following error while running the tracula > pre-processing command and was hoping you could help me understand how > to correct this. > > Selection from log: > > mri_convert /Users/Desktop/Tracula/diffusion_DTI/ > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz > mri_convert /Users/Desktop/Tracula/diffusion_DTI/ > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz > corRead(): can't open file /Users/Desktop/Tracula/diffusion_DTI/COR-.info > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /Users/Desktop/Tracula/diffusion_DTI/... > Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr > 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 > > trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 > > Please let me know if this is not enough information. Thank you for your help. > > Allison > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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] Matching stats in SPSS and QDEC
Hi list, I have done an analysis using QDEC and now I would like to do set up similar statistical analysis in SPSS on some parcellated structures. I have the following setup in QDEC: 2 cohorts (patients, healthy control subjects) Continuous variable : demeaned Age Nuisance Factor: demeaned intracranial volume DODS I'm interested in the effect of age i.e. "differences in the thickness-age correlation between the patients and healthy subjects" . Now my question is if I the following set up would be correct for doing the stats on slopes in SPSS: Univariate General Linear Model Dependent variable: ROI Fixed Factor: group (i.e. patient or healthy control) Covariate: demeaned age AND demeaned intracranial volume and then I also add an interaction term of demeaned_age*group to be the equivalent to the difference between thickness-age correlation in patients vs. healthy subjects that I have in QDEC. Is this correct? Thanks, Nasim ___ 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] mri_glmfit-sim fwhm error
run mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos get cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir SURFACE: subset_average lh log file is lh.lgi.glmdir/cache.mri_glmfit-sim.log cd /study5/aa-scratch/UTAH/freesurfer_final /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Tue Jan 8 14:21:47 CST 2013 Linux tick.keck.waisman.wisc.edu 2.6.32-279.11.1.el6.x86_64 #1 SMP Tue Oct 16 11:16:02 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux gkirk setenv SUBJECTS_DIR /study5/aa-scratch/UTAH/freesurfer_final FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest Original mri_glmfit command line: cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf subset_average lh --cortex --glmdir lh.lgi.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 38.299834 ERROR: cannot find /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/subset_average/lh/cortex/fwhm38/pos/th20/mc-z.csd i ran mri_surf2surf with --fwhm 10 whats the problem here ? thx greg ___ 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] mri_glmfit-sim fwhm error
The 10mm is what you applied, but data will have an intrinsic smoothness, and the final smoothness is a combo of the two. LGI data tends to start out extremely smooth. I would re-run it without smoothing and see what fwhm you get doug On 01/08/2013 03:24 PM, Gregory Kirk wrote: > > > > run > mri_glmfit-sim --glmdir lh.lgi.glmdir --cache 2 pos > > get > > cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf > subset_average lh --cortex --glmdir lh.lgi.glmdir > SURFACE: subset_average lh > log file is lh.lgi.glmdir/cache.mri_glmfit-sim.log > > cd /study5/aa-scratch/UTAH/freesurfer_final > /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim > --glmdir lh.lgi.glmdir --cache 2 pos > > $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ > Tue Jan 8 14:21:47 CST 2013 > Linux tick.keck.waisman.wisc.edu 2.6.32-279.11.1.el6.x86_64 #1 SMP Tue Oct 16 > 11:16:02 CDT 2012 x86_64 x86_64 x86_64 GNU/Linux > gkirk > setenv SUBJECTS_DIR /study5/aa-scratch/UTAH/freesurfer_final > FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest > > Original mri_glmfit command line: > cmdline mri_glmfit --y lh.lgi.10.mgh --fsgd lgi.fsgd dods --C CC.mtx --surf > subset_average lh --cortex --glmdir lh.lgi.glmdir > > DoSim = 0 > UseCache = 1 > DoPoll = 0 > DoPBSubmit = 0 > DoBackground = 0 > DiagCluster = 0 > gd2mtx = dods > fwhm = 38.299834 > ERROR: cannot find > /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/subset_average/lh/cortex/fwhm38/pos/th20/mc-z.csd > > > i ran mri_surf2surf with --fwhm 10 > > whats the problem here ? > > thx > > greg > ___ > 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: 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] Running recon-all with multiple source files
Hi, I would like to try running recon-all for some subjects using two source images in combination. The first image is a FLAIR with dimensions 288x288x30, while the second is a T1 with dimensions 256x256x165. Furthermore, the each FLAIR voxel has dimensions of 0.79x0.79x4.5 mm, while each T1 voxel has dimensions 1x1x1 mm. I tried running the following command: *recon-all -i FLAIR/FLAIR_P4210_S0001.nii -i T1/T1_P4210_S0001.nii -subjid FreeSurfer_FLAIR* But I got the following error message: *ERROR: inputs have mismatched dimensions!* Is there an inbuilt command in FreeSurfer that will override this error message and perform a linear registration of the two images into the same space automatically, or do I need to perform the registration manually before starting with recon-all? Thank you, Deirdre ___ 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] Running recon-all with multiple source files
Hi Dierdre not sure a FLAIR with that thick slices will be very useful, but the typical workflow is to run recon-all with the T1, then when it's done you can run recon-all with a special switch to register and use the FLAIR. Note that this is only in 5.2, which isn't quite out yet (although you could get a beta if you want) cheers Bruce On Tue, 8 Jan 2013, Deirdre O Shea wrote: > Hi, > > I would like to try running recon-all for some subjects using two source > images > in combination. The first image is a FLAIR with dimensions 288x288x30, while > the second is a T1 with dimensions 256x256x165. Furthermore, the each FLAIR > voxel has dimensions of 0.79x0.79x4.5 mm, while each T1 voxel has dimensions > 1x1x1 mm. > > I tried running the following command: > > recon-all -i FLAIR/FLAIR_P4210_S0001.nii -i T1/T1_P4210_S0001.nii > -subjid FreeSurfer_FLAIR > > But I got the following error message: > > ERROR: inputs have mismatched dimensions! > > Is there an inbuilt command in FreeSurfer that will override this error > message > and perform a linear registration of the two images into the same space > automatically, or do I need to perform the registration manually before > starting with recon-all? > > Thank you, > Deirdre > > ___ 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] 回复: 回复: 回复: about ROI to SPSS
Dear doug I used the command: mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1, and the terminal is following: cmdline mri_segstats --i /media/freesurfer1/CT/qdec/Untitled/y.mgh --slabel fsaverage rh control_AA_GG_ba.label --avgwf avg.dat --id 1 sysname Linux hostname psylab-desktop machine x86_64 user psylab Constructing seg from label Loading /media/freesurfer1/CT/qdec/Untitled/y.mgh Vertex Area is 0.501505 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 19 6.91357 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to avg.dat From the above result, can be show 'Vertex Area is 0.501505 mm^3' and the value of my result were 0.752064 0.773072 0.800245, should be the size of volume, not the surface area. these were my opinion, hope you give me some advice, thanks! Bo Xiang At 2013-01-08 09:25:05,"Douglas N Greve" wrote: > >How do you know it is the volume and not surface area? The values will >be whatever are in y.mgh, so if y.mgh has surface area, then the output >will be surface area. > > >On 01/07/2013 07:38 PM, xiangbo_2...@126.com wrote: >> >> I used the command: >> mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf >> avg.dat --id 1. Thanks! >> >> Bo Xiang >> 送自我的HTC One SU >> >> - Reply message - >> 发件人： "Douglas N Greve" >> 收件人： "xiangbo_2010" , "Freesurfer@nmr.mgh.harvard.edu" >> >> 主题： [Freesurfer] 回复: 回复: about ROI to SPSS >> 日期： 周二, 1 月 8 日, 2013 年 01:51 >> >> >> >> >>> what was your command line? >>> >>> On 01/05/2013 01:43 AM, xiangbo_2010 wrote: Dear doug Using the command to only obtain the size of volume from every subject, however, I want to obtain the size of surface area from every subject, what should I do? thanks! Bo Xiang At 2013-01-05 13:12:18,"Douglas Greve" wrote: Drawing the ROI as a label is fine. Just don't transfer the label to each individual subject. The y.mgh is all the data for all the subjects in the fsaverage space (where the label is defined). You can use mri_segstats, something like mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label --avgwf avg.dat --id 1 avg.dat will have one column and number of rows equal to the number of subjects doug On 1/4/13 11:20 PM, xiangbo_2010 wrote: > Dear doug > I am sorry to disturb you again, I still do not know how to > direct obtain the label of two significant clusters, is not to > draw the ROI? thanks! > Bo Xiang > > > > > > At 2013-01-05 06:49:14,"Douglas N Greve" > wrote: > >yes y.mgh > >On 01/04/2013 05:13 PM,xiangbo_2...@126.com wrote: > >> Do you mean input the file of y.mgh to mri_glmfit and run? Thanks! > >> Bo Xiang > >> 发送自我的HTC One SUJ > >> > >> - Reply message - > >> 发件人： "Douglas N Greve" > >> 收件人： > >> 抄送： "freesurfer" > >> 主题： [Freesurfer] 回复: about ROI to SPSS > >> 日期： 周六, 1 月 5 日, 2013 年 05:48 > >> > >> > >> > >> > >>> That technique can yield inconsistent results when the ROI is > small (as > >>> in your case). You are better off extracting the data directly > from the > >>> input to mri_glmfit. This is created by QDEC and is called > y.mgh. This > >>> will be a file with number of frames equal to the number of > subjects. > >>> > >>> doug > >>> > >>> > >>> > >>> > >>> On 01/04/2013 04:13 PM,xiangbo_2...@126.com wrote: > I drawing two ROIs in two clusters, and mapping two labels to > all subjects, following extract the average surface area of two ROIs from > every subject. Anyway, whether have command to direct obtain the label of > two clusters, not to drawing the ROIs from these clusters, then there > have exactly data to be obtained. Thanks! > Ho Xiang > > 发送自我的HTC One SU > > - Reply message - > 发件人： "Douglas N Greve" > 收件人： > 主题： [Freesurfer] about ROI to SPSS > 日期： 周六, 1 月 5 日, 2013 年 02:42 > > > > > > Hi Bo, you need to make sure that you have exactly the same > design > > matrix in SPSS. The design matrix for qdec is Xg.dat in the > output > > directory. How did you extract the data out of the ROIs? > > > > doug > > > > > > >
Re: [Freesurfer] QA Tool Help - Outliers
Hi Efrat, To look for aseg outliers you'll need to generate a aseg lookup table based on all the subjects in your dataset (-gen-asegLUT). Additionally, in the current version some of the labels the script uses are old and no longer appear in the aseg generated by recon-all, so they will be 0 +/- 0. Sorry for the confusion, we are in the process of revamping this tool to make it easier to use and interpret. -Louis On Mon, 7 Jan 2013, Efrat Kliper wrote: Dear FreeSurfer expert, I am using Freesurfer version 5.1.0. After I run the QA Tool and check my data, I am getting 39 outliers or more for each subject. When I look at the AsegMeans and DefaultAsegMeans files in the QATool library, i see that the mean values in these file for each anatomical label are 0s. Is that OK? what files are you checking for outliers against? My results are in agreement with the literature and i believe non of them should be outliers. Any suggestion what might be the problem? Thank you in advance, Efrat ___ 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] QA Tools Snaps Scrambled
Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: Hi- I’ve come across a peculiar behavior with recon_checker, and am hoping someone can shed some light on this. I have used it 100’s of times in the past, but not for about 2 months. I recently processed a large set of cases I wanted to QC. When I ran it, some, but not all, of the snaps were corrupted. Specifically the talairach, aseg, surfs, and all the ‘detailed snaps’, which are basically additional instances of the aforementioned types. The inflated, curv, and parc are all just fine. As the process runs, all images are being displayed in the pop-up windows, and the html page is created. While there have been no system changes which should affect this, I upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the problem. The problem remains. And the problem remains w/ or w/o the flag for detailed snaps. If all of the images were corrupted, I would have certainly concluded something has gone awry with my system. The fact that only some of the images are corrupted makes me scratch my head. Thoughts? Suggestions? Thanks, Wil ___ 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] 回复: 回复: 回复: about ROI to SPSS
Are those 3 numbers the values in the avg.dat file? Why do you think they are volume? In any event, they have the same interpretation as the values in y.mgh On 1/8/13 8:43 PM, xiangbo_2010 wrote: Dear doug I used the command: mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1, and the terminal is following: cmdline mri_segstats --i /media/freesurfer1/CT/qdec/Untitled/y.mgh --slabel fsaverage rh control_AA_GG_ba.label --avgwf avg.dat --id 1 sysname Linux hostname psylab-desktop machine x86_64 user psylab Constructing seg from label Loading /media/freesurfer1/CT/qdec/Untitled/y.mgh Vertex Area is 0.501505 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 19 6.91357 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to avg.dat From the above result, can be show 'Vertex Area is 0.501505 mm^3' and the value of my result were 0.752064 0.773072 0.800245, should be the size of volume, not the surface area. these were my opinion, hope you give me some advice, thanks! Bo Xiang At 2013-01-08 09:25:05,"Douglas N Greve" wrote: > >How do you know it is the volume and not surface area? The values will >be whatever are in y.mgh, so if y.mgh has surface area, then the output >will be surface area. > > >On 01/07/2013 07:38 PM, xiangbo_2...@126.com wrote: >> >> I used the command: >> mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1. Thanks! >> >> Bo Xiang >> 送自我的HTC One SU >> >> - Reply message - >> 发件人： "Douglas N Greve" >> 收件人： "xiangbo_2010" , "Freesurfer@nmr.mgh.harvard.edu" >> 主题： [Freesurfer] 回复: 回复: about ROI to SPSS >> 日期： 周二, 1 月 8 日, 2013 年 01:51 >> >> >> >> >>> what was your command line? >>> >>> On 01/05/2013 01:43 AM, xiangbo_2010 wrote: Dear doug Using the command to only obtain the size of volume from every subject, however, I want to obtain the size of surface area from every subject, what should I do? thanks! Bo Xiang At 2013-01-05 13:12:18,"Douglas Greve" wrote: Drawing the ROI as a label is fine. Just don't transfer the label to each individual subject. The y.mgh is all the data for all the subjects in the fsaverage space (where the label is defined). You can use mri_segstats, something like mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label --avgwf avg.dat --id 1 avg.dat will have one column and number of rows equal to the number of subjects doug On 1/4/13 11:20 PM, xiangbo_2010 wrote: > Dear doug > I am sorry to disturb you again, I still do not know how to > direct obtain the label of two significant clusters, is not to > draw the ROI? thanks! > Bo Xiang > > > > > > At 2013-01-05 06:49:14,"Douglas N Greve" wrote: > >yes y.mgh > >On 01/04/2013 05:13 PM,xiangbo_2...@126.com wrote: > >> Do you mean input the file of y.mgh to mri_glmfit and run? Thanks! > >> Bo Xiang > >> 发送自我的HTC One SUJ > >> > >> - Reply message - > >> 发件人： "Douglas N Greve" > >> 收件人： > >> 抄送： "freesurfer" > >> 主题： [Freesurfer] 回复: about ROI to SPSS > >> 日期： 周六, 1 月 5 日, 2013 年 05:48 > >> > >> > >> > >> > >>> That technique can yield inconsistent results when the ROI is small (as > >>> in your case). You are better off extracting the data directly from the > >>> input to mri_glmfit. This is created by QDEC and is called y.mgh. This > >>> will be a file with number of frames equal to the number of subjects. > >>> > >>> doug > >>> > >>> > >>> > >>> > >>> On 01/04/2013 04:13 PM,xiangbo_2...@126.com wrote: > I drawing two ROIs in two clusters, and mapping two labels to all subjects, following extract the average surface area of two ROIs from every subject. Anyway, whether have command to direct obtain the label of two clusters, not to drawing the ROIs from these clusters, then there have exactly data to be obtained. Thanks! > Ho Xiang > > 发送自我的HTC One SU > > - Reply message - > 发件人： "Douglas N Greve" > 收件人： > 主题： [Freesurfer] about ROI to SPSS > 日期： 周六, 1 月 5 日, 2013 年 02:42 > > > > > > Hi Bo, you need to make sure that you have exactly the same design > > matrix in SPSS. The design matrix for qdec is Xg.dat in the output > > directory. How did you extract the data out of the ROIs? >>
Re: [Freesurfer] 回复: 回复: 回复: about ROI to SPSS
Dear doug In the avg.dat file, where have 61 values which were equal with number of my subjects, however, I used these values in SPSS, there still no signifiant difference, thanks! Bo Xiang At 2013-01-09 11:53:15,"Douglas Greve" wrote: Are those 3 numbers the values in the avg.dat file? Why do you think they are volume? In any event, they have the same interpretation as the values in y.mgh On 1/8/13 8:43 PM, xiangbo_2010 wrote: Dear doug I used the command: mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1, and the terminal is following: cmdline mri_segstats --i /media/freesurfer1/CT/qdec/Untitled/y.mgh --slabel fsaverage rh control_AA_GG_ba.label --avgwf avg.dat --id 1 sysname Linux hostname psylab-desktop machine x86_64 user psylab Constructing seg from label Loading /media/freesurfer1/CT/qdec/Untitled/y.mgh Vertex Area is 0.501505 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 19 6.91357 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to avg.dat From the above result, can be show 'Vertex Area is 0.501505 mm^3' and the value of my result were 0.752064 0.773072 0.800245, should be the size of volume, not the surface area. these were my opinion, hope you give me some advice, thanks! Bo Xiang At 2013-01-08 09:25:05,"Douglas N Greve" wrote: > >How do you know it is the volume and not surface area? The values will >be whatever are in y.mgh, so if y.mgh has surface area, then the output >will be surface area. > > >On 01/07/2013 07:38 PM, xiangbo_2...@126.com wrote: >> >> I used the command: >> mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf >> avg.dat --id 1. Thanks! >> >> Bo Xiang >> 送自我的HTC One SU >> >> - Reply message - >> 发件人： "Douglas N Greve" >> 收件人： "xiangbo_2010" , "Freesurfer@nmr.mgh.harvard.edu" >> >> 主题： [Freesurfer] 回复: 回复: about ROI to SPSS >> 日期： 周二, 1 月 8 日, 2013 年 01:51 >> >> >> >> >>> what was your command line? >>> >>> On 01/05/2013 01:43 AM, xiangbo_2010 wrote: Dear doug Using the command to only obtain the size of volume from every subject, however, I want to obtain the size of surface area from every subject, what should I do? thanks! Bo Xiang At 2013-01-05 13:12:18,"Douglas Greve" wrote: Drawing the ROI as a label is fine. Just don't transfer the label to each individual subject. The y.mgh is all the data for all the subjects in the fsaverage space (where the label is defined). You can use mri_segstats, something like mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label --avgwf avg.dat --id 1 avg.dat will have one column and number of rows equal to the number of subjects doug On 1/4/13 11:20 PM, xiangbo_2010 wrote: > Dear doug > I am sorry to disturb you again, I still do not know how to > direct obtain the label of two significant clusters, is not to > draw the ROI? thanks! > Bo Xiang > > > > > > At 2013-01-05 06:49:14,"Douglas N Greve" > wrote: > >yes y.mgh > >On 01/04/2013 05:13 PM,xiangbo_2...@126.com wrote: > >> Do you mean input the file of y.mgh to mri_glmfit and run? Thanks! > >> Bo Xiang > >> 发送自我的HTC One SUJ > >> > >> - Reply message - > >> 发件人： "Douglas N Greve" > >> 收件人： > >> 抄送： "freesurfer" > >> 主题： [Freesurfer] 回复: about ROI to SPSS > >> 日期： 周六, 1 月 5 日, 2013 年 05:48 > >> > >> > >> > >> > >>> That technique can yield inconsistent results when the ROI is > small (as > >>> in your case). You are better off extracting the data directly > from the > >>> input to mri_glmfit. This is created by QDEC and is called > y.mgh. This > >>> will be a file with number of frames equal to the number of > subjects. > >>> > >>> doug > >>> > >>> > >>> > >>> > >>> On 01/04/2013 04:13 PM,xiangbo_2...@126.com wrote: > I drawing two ROIs in two clusters, and mapping two labels to > all subjects, following extract the average surface area of two ROIs from > every subject. Anyway, whether have command to direct obtain the label of > two clusters, not to drawing the ROIs from these clusters, then there > have exactly data to be obtained. Thanks! > Ho Xiang > > 发送自我的HTC One SU > > - Reply message - > 发件人： "Douglas N Greve" > 收件人： > 主题： [Freesurfer] about ROI to SPSS > 日期： 周六,
Re: [Freesurfer] 回复: 回复: 回复: about ROI to SPSS
are you positive that the SPSS model is exactly the same as the model in QDEC? You can get the design matrix from Xg.dat On 1/8/13 11:15 PM, xiangbo_2010 wrote: Dear doug In the avg.dat file, where have 61 values which were equal with number of my subjects, however, I used these values in SPSS, there still no signifiant difference, thanks! Bo Xiang At 2013-01-09 11:53:15,"Douglas Greve" wrote: Are those 3 numbers the values in the avg.dat file? Why do you think they are volume? In any event, they have the same interpretation as the values in y.mgh On 1/8/13 8:43 PM, xiangbo_2010 wrote: Dear doug I used the command: mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1, and the terminal is following: cmdline mri_segstats --i /media/freesurfer1/CT/qdec/Untitled/y.mgh --slabel fsaverage rh control_AA_GG_ba.label --avgwf avg.dat --id 1 sysname Linux hostname psylab-desktop machine x86_64 user psylab Constructing seg from label Loading /media/freesurfer1/CT/qdec/Untitled/y.mgh Vertex Area is 0.501505 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 19 6.91357 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to avg.dat From the above result, can be show 'Vertex Area is 0.501505 mm^3' and the value of my result were 0.752064 0.773072 0.800245, should be the size of volume, not the surface area. these were my opinion, hope you give me some advice, thanks! Bo Xiang At 2013-01-08 09:25:05,"Douglas N Greve" wrote: > >How do you know it is the volume and not surface area? The values will >be whatever are in y.mgh, so if y.mgh has surface area, then the output >will be surface area. > > >On 01/07/2013 07:38 PM,xiangbo_2...@126.com wrote: >> >> I used the command: >> mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label > --avgwf avg.dat --id 1. Thanks! >> >> Bo Xiang >> 送自我的HTC One SU >> >> - Reply message - >> 发件人： "Douglas N Greve" >> 收件人： "xiangbo_2010","Freesurfer@nmr.mgh.harvard.edu" >> 主题： [Freesurfer] 回复: 回复: about ROI to SPSS >> 日期： 周二, 1 月 8 日, 2013 年 01:51 >> >> >> >> >>> what was your command line? >>> >>> On 01/05/2013 01:43 AM, xiangbo_2010 wrote: Dear doug Using the command to only obtain the size of volume from every subject, however, I want to obtain the size of surface area from every subject, what should I do? thanks! Bo Xiang At 2013-01-05 13:12:18,"Douglas Greve" wrote: Drawing the ROI as a label is fine. Just don't transfer the label to each individual subject. The y.mgh is all the data for all the subjects in the fsaverage space (where the label is defined). You can use mri_segstats, something like mri_segstats --i y.mgh --slabel fsaverage lh yourlabel.label --avgwf avg.dat --id 1 avg.dat will have one column and number of rows equal to the number of subjects doug On 1/4/13 11:20 PM, xiangbo_2010 wrote: > Dear doug > I am sorry to disturb you again, I still do not know how to > direct obtain the label of two significant clusters, is not to > draw the ROI? thanks! > Bo Xiang > > > > > > At 2013-01-05 06:49:14,"Douglas N Greve" wrote: > >yes y.mgh > >On 01/04/2013 05:13 PM,xiangbo_2...@126.com wrote: > >> Do you mean input the file of y.mgh to mri_glmfit and run? Thanks! > >> Bo Xiang > >> 发送自我的HTC One SUJ > >> > >> - Reply message - > >> 发件人： "Douglas N Greve" > >> 收件人： > >> 抄送： "freesurfer" > >> 主题： [Freesurfer] 回复: about ROI to SPSS > >> 日期： 周六, 1 月 5 日, 2013 年 05:48 > >> > >> > >> > >> > >>> That technique can yield inconsistent results when the ROI is small (as > >>> in your case). You are better off extracting the data directly from the > >>> input to mri_glmfit. This is created by QDEC and is called y.mgh. This > >>> will be a file with number of frames equal to the number of subjects. > >>> > >>> doug > >>> > >>> > >>> > >>> > >>> On 01/04/2013 04:13 PM,xiangbo_2...@126.com wrote: > I drawing two RO
Re: [Freesurfer] Matching stats in SPSS and QDEC
Hi Nasim, I don't use SPSS, so I'm not sure I can help, but I think what you have is right but you'll need another factor which is ICV*group. The Xg.dat file contains the design matrix for QDEC, so you might be able to compare it to what you get for SPSS doug On 1/8/13 3:05 PM, Maleki, Nasim wrote: > Hi list, > > I have done an analysis using QDEC and now I would like to do set up similar > statistical analysis in SPSS on some parcellated structures. > > I have the following setup in QDEC: > > 2 cohorts (patients, healthy control subjects) > Continuous variable : demeaned Age > Nuisance Factor: demeaned intracranial volume > DODS > > I'm interested in the effect of age i.e. "differences in the thickness-age > correlation between the patients and healthy subjects" . Now my question is > if I the following set up would be correct for doing the stats on slopes in > SPSS: > > Univariate General Linear Model > Dependent variable: ROI > Fixed Factor: group (i.e. patient or healthy control) > Covariate: demeaned age AND demeaned intracranial volume > > and then I also add an interaction term of demeaned_age*group to be the > equivalent to the difference between thickness-age correlation in patients > vs. healthy subjects that I have in QDEC. Is this correct? > > Thanks, > Nasim > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ 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] unable to download updated mri_segstats
Hi, The link ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux from the release notes for freesurfer 5.1 ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) appears broken. I also checked the anonymous ftp site and found only the directories bbr-papers and growth-curves within the /transfer/outgoing/flat/greve directory. Could someone please direct me to the correct download link for the updated file? Also, is there an updated version of mri_segstats for mac? Thank you. Salil Soman, MD, MS ___ 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.
