Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

mri_glmfit --mask ERROR: dimension mismatch 1 between y and mask
by Mihaela Stefan 22 Jul '16

22 Jul '16

Hello freesurfers, I would like to use mri_glmfit with --mask but I get this error: dimension mismatch 1 between y and mask. I created a binary mask from 22 aparc labels (using mri_binarize) and I would like to run a surface-based analysis only on those regions. The command I use is: mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir lh.group_diff_g2v0.glmdir The input file was generated with this command: mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh >From the error, it seems that I am not using the right input file. What kind of input file should be used with a mask? I also thought to use --label but I am not sure how to combine my 22 labels in one single label. mris_label2annot can combine them but the output is an annotation file not a label. As a note, we will want to do FDR correction, not MC. Thanks! Mihaela

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Fwd: Help with strange 'deprecated' errors with recon-all -i
by Cat Hubbard 22 Jul '16

22 Jul '16

Hi, I am trying to import and recon-all -i my subject files and am getting these strange errors that I have never encountered before. Iteration 1 Tue Jul 19 19:21:54 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.83022/nu0.mnc ./tmp.mri_nu_correct.mni.83022/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.83022/0/ defined(@array) is deprecated at /Applications/freesurfer/mni/bin/nu_estimate_np_and_em line 165. Use of ?PATTERN? without explicit operator is deprecated at /Applications/freesurfer/mni/bin/sharpen_volume line 153. I am trying to reconcile, having looked at various posts I see some mention of this maybe having to do with the version of perl I am using. The version I am currently running is perl 5, version 16, subversion 2 (v5.16.2). I also found other threads with mention of a similar error, and a possible fix but unsure how to implement. Can anyone please help me with this? Thanks!! https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029906.html https://github.com/BIC-MNI/N3/commit/f5a9d0b07369039ac2d1b87e3eb7d73f6fbde7…

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Re: [Freesurfer] Combined parcellation of the left and right hemispheres (Bruce Fischl)
by varshas＠cns.iisc.ernet.in 22 Jul '16

22 Jul '16

> Message: 17 > Date: Thu, 21 Jul 2016 09:31:57 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Combined parcellation of the left and right > hemispheres > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1607210931470.14081(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Varsha > > try using mri_aparc2aseg Hi Bruce, I tried using mri_aparc2aseg. While it gives me one volume file as I wanted, the indices on the volume don't seem to correspond to the look-up table that I created. I created the look-up table from the annotation files for the left and right hemispheres, appropriately changing the indices to make it a continuous list of ROIs. Regards, Varsha > cheers > Bruce > On Thu, 21 Jul 2016, varshas(a)cns.iisc.ernet.in > wrote: > >> >> Hi, >> >> I've been working on getting a finer parcellation of the >> Desikan-Killiany >> atlas using mris_divide_parcellation. I was able to generate two >> annotation files; one each for the left and right hemisphere. I want to >> create a volume similar to aparc+aseg.mgz, containing the labels and >> indices of the ROIs from both hemispheres. I tried using mri_label2vol. >> However, this gives me two separate volumes for the left and right >> hemispheres. Is there a way to combine these volumes into one? >> Alternatively, can one generate such a volume form an annotation file >> that >> has information of both hemispheres? >> >> Any help is greatly appreciated! >> >> Regards, >> Varsha >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > ------------------------------ > > Message: 18 > Date: Thu, 21 Jul 2016 09:33:29 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Freesurfer build stamps do not match > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1607210932310.14081(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Subin > > it looks more likely that you just don't have write access to your > SUBJECTS_DIR. Can you check that with ls -l? Or maybe you just haven't set > it and it still points to the one we distribute? Typically you want to set > the SUBJECTS_DIR env variable to some other directory where you will store > all the subjects in a study. > > cheers > Bruce > > > On Thu, 21 Jul 2016, Lee > Subin Kristine wrote: > >> >> Hi FreeSurfer Team, >> >> >> After I have downloaded the FreeSurfer dev version, I get the following >> error >> whenever I use the recon-all comand: >> >> >> mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': >> Permission >> denied >> mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': >> Permission >> denied >> mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': >> Permission >> denied >> cp: cannot create regular file >> '/usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt': No such >> file or >> directory >> cat: /usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt: No such >> file or >> directory >> INFO: FreeSurfer build stamps do not match >> Subject Stamp: >> Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 >> /usr/local/freesurfer/subjects/NYS/scripts/patchdir.txt: No such file or >> directory. >> >> recon-all used to work fine when I used the stable 5.3 version. >> I think it may have something to do with the fact that I previously ran >> recon-all >> in v.5.3, and so the current subject directory's stamp is still 5.3 (or >> blank..) >> and it does not match the current stamp of the dev version? I am not >> sure.. >> Could anyone tell me how I can fix this problem? >> >> Thanks in advance, >> Subin >> >> >> > > > ------------------------------ > > Message: 19 > Date: Thu, 21 Jul 2016 09:35:35 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Subtracting overlays > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1607210933500.14081(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-15" > > Hi Tobias > > yes, mris_calc should do it. If you give the output extension .mgz it will > save in that format instead of curv I believe (and will work fine as an > overlay) > > cheers > Bruce > > > On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote: > >> Hi,? >> Is there a way to subtract one surface overlay from another (for example >> in >> fsaverage) and still having the output being an .mgh overlay file?? >> I saw that mis_calc does a similar procedure but automatically outputs >> the result >> as out.mgz.? >> >> Thank you for the help!? >> >> Kind regards, >> Tobias >> ? >> _________________________________________? >> Tobias Granberg, MD, PhD? >> >> Post-doctoral research fellow >> A.A. Martinos Center for Biomedical Imaging? >> Massachusetts General Hospital | Harvard Medical School >> >> Resident in Radiology? >> Karolinska Institutet | Department of Clinical Science, Intervention and >> Technology >> Karolinska University Hospital | Department of Radiology >> >> > > ------------------------------ > > Message: 20 > Date: Thu, 21 Jul 2016 13:42:48 +0000 > From: "Granberg, Erik Tobias" <EGRANBERG(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Subtracting overlays > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <9294313C-F63A-420D-BF9C-D568A9A7B21D(a)mgh.harvard.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Bruce, > > Great, thanks for the quick reply! That worked beautifully. I was > apparently using the wrong output option. > Much appreciated! > > Kind regards, > Tobias > > _________________________________________ > Tobias Granberg, MD, PhD > > Post-doctoral research fellow > A.A. Martinos Center for Biomedical Imaging > Massachusetts General Hospital | Harvard Medical School > > Resident in Radiology > Karolinska Institutet | Department of Clinical Science, Intervention and > Technology > Karolinska University Hospital | Department of Radiology > > > On 21 jul 2016, at 09:35, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > Hi Tobias > > yes, mris_calc should do it. If you give the output extension .mgz it will > save in that format instead of curv I believe (and will work fine as an > overlay) > > cheers > Bruce > > > On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote: > > Hi, > Is there a way to subtract one surface overlay from another (for example > in > fsaverage) and still having the output being an .mgh overlay file? > I saw that mis_calc does a similar procedure but automatically outputs the > result > as out.mgz. > Thank you for the help! > Kind regards, > Tobias > > _________________________________________ > Tobias Granberg, MD, PhD > Post-doctoral research fellow > A.A. Martinos Center for Biomedical Imaging > Massachusetts General Hospital | Harvard Medical School > Resident in Radiology > Karolinska Institutet | Department of Clinical Science, Intervention and > Technology > Karolinska University Hospital | Department of Radiology > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Superimposing average hippocampal colume onto a betted brain
by Dr Sampada Sinha 22 Jul '16

22 Jul '16

Dear freesurfer experts, Thank you for guiding me on how to create average volume of all subjects of depression patients. I later binarized the average volume generated to extract the amygdala and hippocampus volume(Right and left). Please find attached. How do I superimpose the extracted amygdala and hippocampus on to the betted image using freesurfer commands? I am trying to reproduce the following image as an example. (Can I use vol2vol command?) Greatly appreciate all your help. Thanks and regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

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PhD position in structural imaging in First Episodes of Non-Affective Psychosis
by Diana Tordesillas-Gutiérrez 22 Jul '16

22 Jul '16

"PhD position in structural imaging in First Episodes of Non-Affective Psychosis" A four years funded full-time PhD position will be available at the Neuroimaging Unit – Health Research Institute Valdecilla (IDIVAL) headed by Professor Benedicto Crespo- Facorro from October 2016. We are seeking for a highly motivated individual with experience in brain imaging and computational/statistical background to take a leading role in structural neuroimaging analysis. The candidate should hold a degree in psychology, biology, neuroscience or a related field. This work will be co-directed by Prof. B Crespo-Facorro (Psychiatrist) and Dr. D Tordesillas-Gutiérrez (Physicist). Salary is according to Spanish standards. Interested candidates should send their CV along with a letter of motivation and their detailed marks during their Master (or latest achieved degree) to Dr. Diana Tordesillas-Gutiérrez, e-mail: diana.tordesillas(a)humv.es ------------------------------------------------------------------------------------------------------------------------------ Diana Tordesillas Gutiérrez, PhD Neuroimaging Unit IDIVAL IDIVAL Building Avda. Cardenal Herrera Oria s/n 39011 Santander Spain Tel. +34 942202677 diana.tordesillas(a)humv.es diana.tordesillas(a)gmail.com ------------------------------------------------------------------------------------------------------------------------------

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aparc+aseg.mgz for network analysis
by Jinsong Tang 21 Jul '16

21 Jul '16

Hello freesurfers, I want to select the subcortical structures (thalamus, pallidum, caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as nodes of the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035]. However, in the aparc+aseg.mgz files, there are also some other labels. Is there any way to delete all other unselected labels? Thank you so much! Best, Jinsong

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question about image size
by Dorsa Haji Ghaffari 21 Jul '16

21 Jul '16

Hi, I have segmented 288 slices of 512x512 dicom MRIs but when I create a mask of the left thalamus I get 256 slices of 256x256 images. Is there any way to get the same number of slices with the same size as I had before? Thank you Dorsa

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registering subject pial to fsaverage
by Trisanna Sprung-Much 21 Jul '16

21 Jul '16

Hi there I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data. Below is the command that I ran. Is there something I am missing here? many thanks Trisanna trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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'Cerebral Exterior' label in Freeview but not tkmedit
by Uquillas, Federico D'Oleire 21 Jul '16

21 Jul '16

Dear FreeSurfer community, Despite tkmedit being discontinued, I am still using this to make surface edits to my T1s. The main reason is that when I use Freeview and erase skull/dura, Freeview creates this blue label wherever I erase outside of the brain surface. The label is called left (or right) ‘-Cerebral-Exterior’. If I edit in tkmedit, this label is not created. I fear that this label may cause problems if the list of labels in FreeSurfer (particularly 5.1) does not contain this ‘Cerebral Exterior’ label. I suppose this has been addressed in the more recent developments, and theoretically if I use FreeSurfer 6 to process and Freeview to edit then this wouldn’t be a concern. Wondering if anyone has encountered this, and whether it was a problem or not for you. Thank you so much as always for any thoughts or recommendations you may be able to provide. Best, Fred

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Subtracting overlays
by Granberg, Erik Tobias 21 Jul '16

21 Jul '16

Hi, Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz. Thank you for the help! Kind regards, Tobias _________________________________________ Tobias Granberg, MD, PhD Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology

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Freesurfer July 2016