Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

paired ttest by specifying file names
by Dace Apšvalka 14 Oct '15

14 Oct '15

Hi, I am not entirely sure I am doing it right, therefore would like to have a confirmation if possible. I am runing a paired ttest between two conditions by specifying file names. Here is an example of 2 subjects mris_preproc \ --target fsaverage \ --hemi lh \ --out /ResultsDir/lh.outfilename.mgh \ --fsgd pairs.fsgd \ --is /subject1/condition1.mgh \ --is /subject1/condition2.mgh \ --is /subject2/condition1.mgh \ --is /subject2/condition2.mgh \ --srcfmt curv \ --paired-diff mri_surf2surf --s fsaverage \ --hemi lh \ --fwhm 5\ --sval /ResultsDir/lh.outfilename.mgh \ --tval /ResultsDir/lh.outfilename.sm05.mgh mri_glmfit \ --glmdir /ResultsDir \ --y /ResultsDir/lh.outfilename.sm05.mgh \ --fsgd paired-diff.fsgd \ --C mean.mtx \ --surf fsaverage lh \ --cortex %% my pairs.fsgd file GroupDescriptorFile 1 Title StudyTitle Class Main Input subject1 Main Input subject1 Main Input subject2 Main Input subject2 Main %% my paired-diff.fsgd GroupDescriptorFile 1 Title StudyTitle Class Main Input subject1 Main Input subject2 Main %% my mean.mtx file 1 Thanks, Dace

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Problem with fsgd file
by Bronwyn Overs 14 Oct '15

14 Oct '15

Dear mailing list, I am trying to run a longitudinal 2 stage model using mri_glmfit. Here is the command I am using: mri_glmfit --fsgd long-2stage_ConAR.fsgd --glmdir long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh dods --C me_age-all.mtx --C me_gender.mtx --C me_group.mtx --C int_ageXgroup.mtx --C int_ageXgender.mtx --C int_genderXgroup.mtx --C int_ageXgenderXgroup.mtx --surf fsaverage lh --label long-ConAR.lh.area.fsaverage.cortex.label However, when I try to run the command it has problems reading my fsgd file. I have attached my file for reference and here are the errors it spits out: gdfReadHeader: reading long-2stage_ConAR.fsgd INFO: ignoring tag 7541001001 INFO: ignoring tag 7541002001 INFO: ignoring tag 7541003001 INFO: ignoring tag 7541006001 INFO: ignoring tag 7541009001 INFO: ignoring tag 7541011004 INFO: ignoring tag 7541012004 INFO: ignoring tag 7541017001 INFO: ignoring tag 7541018001 INFO: ignoring tag 7541020001 INFO: ignoring tag 7541022001 INFO: ignoring tag 7541023001 INFO: ignoring tag 7541024001 INFO: ignoring tag 7541026001 INFO: ignoring tag 7541030001 INFO: ignoring tag 7541031001 INFO: ignoring tag 7541036001 INFO: ignoring tag 7541040001 INFO: ignoring tag 7541041001 INFO: ignoring tag 7541042001 INFO: ignoring tag 7541044001 INFO: ignoring tag 7541046001 INFO: ignoring tag 7541047001 INFO: ignoring tag 7541048004 INFO: ignoring tag 7541049001 INFO: ignoring tag 7541052001 INFO: ignoring tag 7541055001 INFO: ignoring tag 7541057001 INFO: ignoring tag 7541058001 INFO: ignoring tag 7541059001 INFO: ignoring tag 7541060001 INFO: ignoring tag 7541062001 INFO: ignoring tag 7541070001 INFO: ignoring tag 7541075001 INFO: ignoring tag 7541078001 INFO: ignoring tag 7541080001 INFO: ignoring tag 7541084001 INFO: ignoring tag 7541085001 INFO: ignoring tag 7541088001 INFO: ignoring tag 7541090001 INFO: ignoring tag 7541093001 INFO: ignoring tag 7541094001 INFO: ignoring tag 7541096001 INFO: ignoring tag 7541097004 INFO: ignoring tag 7541099001 INFO: ignoring tag 7541100001 INFO: ignoring tag 7541101001 INFO: ignoring tag 7541102001 INFO: ignoring tag 7541103001 INFO: ignoring tag 7541106001 INFO: ignoring tag 7541108001 INFO: ignoring tag 7541110004 INFO: ignoring tag 7541112001 INFO: ignoring tag 7541114001 INFO: ignoring tag 7541116001 INFO: ignoring tag 7541118001 INFO: ignoring tag 7541119001 INFO: ignoring tag 7541120001 INFO: ignoring tag 7541124001 INFO: ignoring tag 7541125001 INFO: ignoring tag 7541132004 INFO: ignoring tag 7541133001 INFO: ignoring tag 7541139001 INFO: ignoring tag 7541142001 INFO: ignoring tag 7541143001 INFO: ignoring tag 7541146001 INFO: ignoring tag 7541149001 INFO: ignoring tag 7541150001 INFO: ignoring tag 7541151001 INFO: ignoring tag 7541156001 INFO: ignoring tag 7541161001 INFO: ignoring tag 7541165001 INFO: ignoring tag 7541168001 INFO: ignoring tag 7541175001 INFO: ignoring tag 7541177001 INFO: ignoring tag 7541178001 INFO: ignoring tag 7541182001 INFO: ignoring tag 7541185001 INFO: ignoring tag 7541188001 INFO: ignoring tag 7541190004 INFO: ignoring tag 7541192004 INFO: ignoring tag 7541196001 INFO: ignoring tag 7541198001 INFO: ignoring tag 7541209001 INFO: ignoring tag 7541223001 INFO: ignoring tag 7541227001 INFO: ignoring tag 7541334001 INFO: ignoring tag 7541337001 INFO: ignoring tag 7541345001 INFO: ignoring tag 7541346001 INFO: ignoring tag 7541353001 INFO: ignoring tag 7541366001 INFO: ignoring tag 7541378001 INFO: ignoring tag 7541383001 INFO: ignoring tag 7541388001 INFO: ignoring tag 7541391001 INFO: ignoring tag 7541396001 INFO: ignoring tag 7541400001 INFO: ignoring tag 7541401001 INFO: ignoring tag 7541402001 INFO: ignoring tag 7541409001 INFO: ignoring tag 7541411001 INFO: ignoring tag 7541412001 INFO: ignoring tag 7541421001 INFO: ignoring tag 7541442004 INFO: ignoring tag 7541443001 INFO: ignoring tag 7541445001 WARNING: gdfReadV1: class genderM-groupCtl is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 years -nan -nan 1 age_mc -nan -nan Class Means of each Continuous Variable 1 genderM-groupCtl -nan -nan 2 genderF-groupCtl -nan -nan 3 genderM-groupAR -nan -nan 4 genderF-groupAR -nan -nan INFO: gd2mtx_method is dods ERROR: Option dods unknown Can you tell me what is wrong? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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No preprocessing on FAST
by stdp82＠virgilio.it 14 Oct '15

14 Oct '15

Hi list, I'd like to perform FAST preprocessing for functional connectivity (seed-based analysis).Data have been already preprocessed by AFNI.Therefore, no smoothing, motion and slice timing corrections are requested. When I run:preproc-sess -sf sessid -nomc -fwhm 0 -surface fsaverage lhrh -mni305-1mm -fsd rest -per-run -nostc the analysis is stopped by an error on lacking fmcpr.nii. Thanks Best regards, Stefano Sent from Virgilio Mobile

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Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache
by Selvaraj, Bhavani 14 Oct '15

14 Oct '15

Hi Martin, Thanks martin for your reply. I am also running v5.3 I am trying to run this command the command works fine for LH only when I run RH it fails long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR I am sending the 3 label file please let me if this is the right input file you need 1. MPS-007_1.long.MPS-007/label/rh.cortex.label 2. MPS-007/label/rh.long.cortex.label 3. MPS-007/label/rh.long.cortex.label The same command for the lh worked fine for this particular subject. I was able to solve the qdec error. This one I am unable to. Thanks , Bhavani This what I get from my terminal window. freesurfer% long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Parsing the qdec table: /Applications/freesurfer/subjects/qdec/long.qdec.table.dat Working in SUBJECTS_DIR: /Applications/freesurfer/subjects Working on hemi: rh Subject-Template: MPS-007 INFO: 3 TPs in MPS-007 , mean age: 3.66666666667 =============================================================================== SUBJECT MPS-007 Intersecting Within-Subject Cortex Label cp /Applications/freesurfer/subjects/MPS-007_1.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label mris_label_calc intersect /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label ERROR -11 : mris_label_calc intersect did not work? [mcradxym9290:~] freesurfer% mris_label_calc intersect /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label Segmentation fault [mcradxym9290:~] freesurfer% ________________________________________ From: Martin Reuter [mreuter(a)nmr.mgh.harvard.edu] Sent: Tuesday, October 13, 2015 3:24 PM To: freesurfer(a)nmr.mgh.harvard.edu Cc: Selvaraj, Bhavani Subject: Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache Hi Bhavani, when I run mris_label_calc intersect MPS-007_2mod.long.MPS-007\ rh.cortex.label MPS-\ 007\ lh.cortex.label out.label it goes through and writes the out.label file. I used fs 5.3 for that. Can you please send me the command and input files that fail for you? About your other questions: qdec tables should be stored in <SUBJECS_DIR>/qdec not sure about the other error. can you send the cross qdec table. probably you need a level file for group? Thanks, Martin P.S. Please post questions to the FreeSurfer list. On 10/13/2015 10:56 AM, Selvaraj, Bhavani wrote: > Hi Martin, > Thanks for the reply. Yes those files are available at these locations. > when I run this command for LH > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label > --time years --qcache fsaverage --sd $SUBJECTS_DIR it runs smoothly > and gave me these results tksurfer MPS-007 lh pial -overlay > /Applications/freesurfer/subjects/MPS-007/surf/lh.long.thickness-avg.f > whm25.mgh tksurfer MPS-005 lh pial -overlay > /Applications/freesurfer/subjects/MPS-005/surf/lh.long.thickness-avg.f > whm25.mgh > > but for the rh only the patients MPS-007 gave me the error MPS-005 worked fine. > How do I fix that? > I am attaching you the cortex label file I don't know how to tell if it is corrupted. > > Also I have two more question where should I store the QDEC data table > Is this where I should make it? > Applications/freesurfer/subjects/qdec/ long.qdec.table.dat > > also when I try to open the table in Qdec I get the following error: > freesurfer% qdec --table ./qdec/cross.qdec.table.dat > > Reading /Applications/freesurfer/tktools/tkUtils.tcl > > Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > > Loading data table ./qdec/cross.qdec.table.dat... > Number of columns: 13 > fsid column: 1 > Number of factors: 12 > Number of subjects: 2 > ERROR: QdecSubject::GetContinuousFactor failure: could not find factor > name: Group for subject MPS-007 > > Thanks Martin for your help! > bhavani > > > ________________________________________ > From: Martin Reuter [mreuter(a)nmr.mgh.harvard.edu] > Sent: Friday, October 09, 2015 8:59 PM > To: Selvaraj, Bhavani > Subject: Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache > > Hi Bhavani, > > Strange, are those files available at those locations? Can you also check permissions. Open the label files to see if they are corrupted. > Best MartinOn Oct 9, 2015 11:31 AM, "Selvaraj, Bhavani" <Bhavani.Selvaraj(a)nationwidechildrens.org> wrote: >> Hi, >> >> when I try running longitudinal analysis for 2 subjects I get the >> following error (this error >> >> only persists for the right hemisphere-- left hemisphere works fine for this subject). >> >> >> >> mris_label_calc intersect >> /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh. >> cortex.label >> /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label >> /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label >> >> >> >> ERROR -11 : mris_label_calc intersect did not work? >> >> I saw a similar question in the archived mail list so I tried running >> this command by itself and this was the comment >> >> Segmentation fault >> >> I didn't know how to fix this error? should I run them again?? >> >> >> >> >> >> Qdec table >> >> Fsid fsid-base years >> >> MPS-007_1 MPS-007 3 >> >> MPS-007_2mod MPS-007 4 >> >> MPS-007_3 MPS-007 4 >> >> MPS-005_1 MPS-005 5 >> >> MPS-005_2 MPS-005 6 >> >> MPS-005_3 MPS-005 6 >> >> >> >> >> >> Thanks, >> >> Bhavani > > 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_c > omplianceline&d=BQIGaQ&c=FGzDrZ8hK6OoO1oc9Smc5viw6E0cF__gglPkcFwC2N8&r=ffK64aaMIE1GqLjcz0w1FGZ_6Mr7vi1gDBqjGMI4TaEnGxgSIdq3bd_mOh9MSBnd&m=Hs6n9odtXPNNWQ9Dlp9yZKsYEEJqQzj6Z5qx7CPJzQg&s=_Iw44QDPyqCDPAS553jTtLhz8MykhvP44nRqVJmcZTQ&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. -- 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 : https://urldefense.proofpoint.com/v2/url?u=http-3A__reuter.mit.edu&d=BQIF-g… 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_compli… . 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.

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Re: [Freesurfer] unusually long running time in autorecon2
by Bruce Fischl 14 Oct '15

14 Oct '15

Hi David it works fine for me. The infinte loop happened when the brainmask was completely empty I believe, although we fixed it in any case. Can you check the brainmask? I can also send you an updated mri_cc if you want cheers Bruce On Mon, 12 Oct 2015, Slater David wrote: > > Hi Bruce, > > > > I’ve also run into the ‘infinite loop problem’ mentioned here:https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/02…. > html > > > > 30 of my 632 subject’s experienced this problem. In your post you asked for > an example file which generates this failure. I have included such a file as > an attachment along with the full job log up to the point where it hung. > > > > I am running freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and use the > simple command recon-all -subjid <SubjectID> -all. > > > > Cheers, > > David > > >

1 0

Talairach Conversion
by Ishan Patel 14 Oct '15

14 Oct '15

Hello, I wanted to use the function: mri_label2label to convert my label file into talairach space. This is the output that I am getting. On the mri_label2label information page, it says to use 'talairach' as the target subject which is what I did, but it cannot find 'talairach'. Does anyone have experience with this? [image: Inline image 1]

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Re: [Freesurfer] Segmentation fault using mri_label2vol
by Syeda Maryam 14 Oct '15

14 Oct '15

So for some reason my mail with the attachments won't get delivered...the message size exceeds the limits. I was wondering if the segmentation fault error I'm getting might be do to some problem in the freesurfer version I'm running? Thanks,Syeda On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam <swajiham(a)yahoo.com> wrote: I'm not sure if my last message got delivered or not so I'll resend it. Thanks very much for looking into this so quickly. Sure thing! I've attached the images here. The aseg file opens up with freeview, and the mri_label2vol command works fine on my local machine but when I try to implement it on our server using nipype, it gives me the error I mentioned. Best, Syeda On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam <swajiham(a)yahoo.com> wrote: Thanks very much for looking into this so quickly. Sure thing! I've attached the images here. The aseg file opens up with freeview, and the mri_label2vol command works fine on my local machine but when I try to implement it on our server using nipype, it gives me the error I mentioned. Best,Syeda On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Syeda that commnand doesn't segfault when I try it on another subject here. If you email me the aseg.mgz and the rawavg.mgz I'll take a look cheers Bruce On Wed, 14 Oct 2015, Syeda Maryam wrote: > Hello Freesurfer experts, > > I'm getting a segmentation fault when I use the mri_label2vol command to push aseg labels from freesurfer space to my > subject's original T1 space (using the example given on the freesurfer website). I'm not sure why this is > happening...I've tried changing the parameters countless times but nothing has worked. I also checked my "aseg.mgz" to > make sure it's not corrupted but that isn't the issue either. Any help would be highly appreciated!! Thanks in advance > > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz > Number of labels: 0 > Annot File: (null) > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz > Registration File: (null) > Fill Threshold: 0 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > LabelCodeOffset 0 > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ > Template RAS-to-Vox: -------- > -0.985 0.000 0.000 128.000; > -0.000 -0.000 -0.985 128.000; > -0.000 0.833 -0.000 98.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1.23773 > nHits Thresh: 0 > Computing registration based on header > RegMat: -------- > 1.000 0.000 0.000 -0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -0.985 0.000 0.000 128.000; > 0.000 0.000 -0.985 128.000; > 0.000 0.833 0.000 98.000; > 0.000 0.000 0.000 1.000; > ASeg2Vol: Building LUT > Segmentation fault > > > 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.

2 4

Segmentation fault using mri_label2vol
by Syeda Maryam 14 Oct '15

14 Oct '15

Hello Freesurfer experts, I'm getting a segmentation fault when I use the mri_label2vol command to push aseg labels from freesurfer space to my subject's original T1 space (using the example given on the freesurfer website). I'm not sure why this is happening...I've tried changing the parameters countless times but nothing has worked. I also checked my "aseg.mgz" to make sure it's not corrupted but that isn't the issue either. Any help would be highly appreciated!! Thanks in advance mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -0.985 0.000 0.000 128.000; -0.000 -0.000 -0.985 128.000; -0.000 0.833 -0.000 98.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1.23773 nHits Thresh: 0 Computing registration based on header RegMat: -------- 1.000 0.000 0.000 -0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.985 0.000 0.000 128.000; 0.000 0.000 -0.985 128.000; 0.000 0.833 0.000 98.000; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT Segmentation fault

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Segmentation fault using mri_label2vol
by Syeda Wajiha Maryam 14 Oct '15

14 Oct '15

1 0

pial surface encircling the optical chiasm
by Antonin Skoch 14 Oct '15

14 Oct '15

Dear FreeSurfer experts, during inspection of reconstructions of our data, I found that in many cases the pial (and sometimes also white) surface is extending out of the brain and encircling the optical chiasm. Does this situation has any effect to the results (i.e. cortex parcellation, whole-brain group thickness or local gyrification index analysis), i.e. is it an reconstruction error which should be manually corrected? Or can we safely ignore it? Regards, Antonin Skoch

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