Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

question(s) about brain volume calculation
by Golchin, Nima 12 Jul '10

12 Jul '10

I was wondering how FreeSurfer calculates brain volume. Is volume calculated from the voxels included in brainmask.mgz, from the area inside the generated Pial surface, or from summing the aseg volume statistics? Also, to exclude ventricular volume, do you just subtract the segmented ventricle label volume? I ask because I was wondering what freesurfer errors I should be concerned about most when looking at whole brain volume (pial surface including eye/skull, overzealous segmentation labeling, etc). Also, how should I consider whole brain volume regarding the difficulties freesurfer has calculating the surface of the hippocampus. Thanks for your help. -Nima

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Making Average Subject
by nitenson＠nmr.mgh.harvard.edu 12 Jul '10

12 Jul '10

Hi, I'm a newcomer to Freesurfer and I'm having problems trying to create an average subject from a subset of our patients. I used the command "make_average_surface --fsgd y.fsgd" with y.fsgd basically being a copy of an old fsgd file with a few subjects deleted. The process ran for several hours (I had to let it run over the weekend) and seemed to be processing the 12 subjects that I wanted. However when I tried to open it today with "tksurfer 12AboveChanceAvg lh inflated", I get the following message: surfer: current subjects dir: /space/sake/3/users/inverse/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/homes/006/nitenson ERROR: could not read header info from T1 or orig in /space/sake/3/users/inverse/subjects/12AboveChanceAvg/mri I noticed that the mri folder in the new average I created only has one mgz file (mni305.cor.mgz) while the mri folder in fsaverage has many more. I am currently running make_average_subject --fsgd y.fsgd, but it seems that it's starting to produce the same results. What is the best way to create an average subject on which to study functional overlays? Thanks, Adam Nitenson Brain Genomic Lab

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affine matrix
by Xu, Jun 12 Jul '10

12 Jul '10

Hi, I was trying to create affine matrix from DICOM file and compared with the one created by mri_convert. For T1 image, if I use mri_convert >mri_convert -it dicom [in filename] -ot nii [out filename] The affine matrix (srow*) part get from load_nii_hdr.m command is Affine I: srow_x: [0 0 -1.2000 92.2031] srow_y: [-1 0 0 132.7965] srow_z: [0 -1 0 131.8291] which is the same affine matrix I got directly from DICOM file according to the description in nifti header doc. However, if I use >mri_convert -it dicom [in filename] -ot nii [out filename] -out_orientation PRS The affine matrix (srow*) part get from load_nii_hdr.m command is Affine II: srow_x: [1 0 0 -123.7969] srow_y: [0 -1 0 140.7965] srow_z: [0 0 1.2000 -92.1709] That I do not know how to create. I know the orientation is changed from PSR (T1 sag original) to RPS (specified in out_orientation). Could you tell me what I can do in order to obtain an affine matrix II from affine I? Thanks. Jun

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Linear regression
by Dankner, Nathan (NIH/NIMH) [F] 12 Jul '10

12 Jul '10

Hi All, I sent this last week and it may have slipped through the cracks. I have a dataset with two subject groups. I'm looking to see if there are different age effects on cortical thickness by diagnosis. Initially we did this by testing the interaction of two categorical variables, diagnosis and age (with a median split on age). We are now trying to look at this with age as a continuous variable, but QDEC seemingly does not allow you to look at interactions with continuous variables. Is there a way of doing this using the command line? I've looked at the Group Analysis tutorial, but haven't been able to satisfactorily answer this question. Any help would be appreciated. Thanks, Nathan

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Troubleshooting: Are these pial and wm surface acceptable?
by xuemei lei 12 Jul '10

12 Jul '10

Hi All I recently started with FreeSurfer, and I am not sure about the pial and wm surface in the subcortical regions( eg. Hippocampus and amygdala,Medial temporal lobe). I have attatched the figures. Are these pial and wm surfaces acceptable? I have no ideas about the criterion and the right surface in this regions reconstracted by Freesurfer. Please let me know! thank you very much! -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 Email: bnuxuemei(a)gmail.com Blog: www.dubo.in Web: http://psychbrain.bnu.edu.cn ============================================== Welcome to the Blog: www.dubo.in

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HELP
by Asaf Kaftory 12 Jul '10

12 Jul '10

unsubscribe me thanks. ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Mon, July 12, 2010 8:09:19 AM Subject: Freesurfer Digest, Vol 77, Issue 22 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Displaying significant difference with a threshold of cluster size (Douglas N Greve) 2. Re: Displaying significant difference with a threshold of cluster size (liang wang) 3. Troubleshooting: Are these pial and wm surface acceptable? (xuemei lei) ---------------------------------------------------------------------- Message: 1 Date: Sun, 11 Jul 2010 13:42:39 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Displaying significant difference with a threshold of cluster size To: liang wang <wanglbit(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4C3A028F.7070800(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed You should correct for multiple comparisons using cluster-wise correction. See the tutorials on group analysis on our wiki. doug liang wang wrote: > Hi, > > Using mri_glmfit, I found significant between-group difference in > cortical thickness in some regions. However, there are a lot regions > with very small vertices surviving the given threshold. What I need to > do is displaying large clusters (e.g. having 20 vertices at least) > assumed as "true" difference. I don't know how to make it by a > selected threshold of cluster size . Any suggestions would be appreciated. > > Liang > > -- > Liang Wang, PhD > Postdoctoral Fellow > Woodward Lab > Department of Psychiatry > University of British Columbia > BC Mental Health & Addiction Services > 938 West 28th Avenue > Vancouver BC V5Z 4H4 > Telephone: 1-604-875-2000 (ext. 4735) > Fax: 1-604-875-3871 > Email: wanglbit(a)gmail.com <mailto:wanglbit@gmail.com> > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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 ------------------------------ Message: 2 Date: Sun, 11 Jul 2010 11:16:17 -0700 From: liang wang <wanglbit(a)gmail.com> Subject: Re: [Freesurfer] Displaying significant difference with a threshold of cluster size To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <AANLkTinU0knZdFiivSrtnnF4LuV_SlK5iH7eftriOV1-(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello Doug, Thanks for your kind response. I have tried to use mri_glmfit-sim to correct the results. However, no significant differences were observed. To compare with other studies, I would like to report the results (p < 0.001, uncorrected) and mention that they will disappear if corrected by cluster-based threshold method. Is it a acceptable way? Liang 2010/7/11 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > You should correct for multiple comparisons using cluster-wise correction. > See the tutorials on group analysis on our wiki. > > doug > > liang wang wrote: > >> Hi, >> >> Using mri_glmfit, I found significant between-group difference in cortical >> thickness in some regions. However, there are a lot regions with very small >> vertices surviving the given threshold. What I need to do is displaying >> large clusters (e.g. having 20 vertices at least) assumed as "true" >> difference. I don't know how to make it by a selected threshold of cluster >> size . Any suggestions would be appreciated. >> >> Liang >> >> -- >> Liang Wang, PhD >> Postdoctoral Fellow >> Woodward Lab >> Department of Psychiatry >> University of British Columbia >> BC Mental Health & Addiction Services >> 938 West 28th Avenue >> Vancouver BC V5Z 4H4 >> Telephone: 1-604-875-2000 (ext. 4735) >> Fax: 1-604-875-3871 >> Email: wanglbit(a)gmail.com <mailto:wanglbit@gmail.com> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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 > > -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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Troubleshooting: Are these pial and wm surface acceptable?
by xuemei lei 11 Jul '10

11 Jul '10

1 0

FDR correction in Qdec
by Xiaojing Long 10 Jul '10

10 Jul '10

Hi, all, I have some questions about performing the FDR correction in Qdec. I ran recon-all on all my subjects, then ran the surface group analysis following the Qdec tutorial. There are 3 factors in the qdec.table.dat file: age, gender and diagnosis. In the Design tab of Qdec, I selected the discrete factor 'diagnosis' for analysis. When the analysis was done, there is a description "Does the average thickness differ between Diseased and Normal?" in the Display tab. I think this should be the uncorrected map. Then I tried to run the FDR correction for multiple comparisons. I set the rate to be 0.05 and 0.01 respectively. However, I found no difference between the results using different rates. In the Terminal, the information are also the same: "MRISfdr2vwth(): np = 163842, nv = 163842 Found 107008 of 163842 vertices above FDR threshold (of 1.48619)" I wonder whether I did the analysis correctly. Are such results possible or reasonable? Thank you in advance. Best, Xiaojing

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left right reversal
by YUMI MAEDA 09 Jul '10

09 Jul '10

Hi, I am trying to do left right reversal of surface by following this link, http://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal?highlight=(rever… after recon-all -subcortseg -s LRflipped-subject", I tried to check the result with tksurfer with 'tksurfer LRflipped-subject hemi inflated'. Then I got this error message that MRISread(/freesurfer//LRflipped-subject/surf/lh.inflated): could not open file No such file or directory tksurfer.bin: could not read surface file /freesurfer//LRflipped-subject/surf/lh.inflated. No such file or directory Here is my question, Is this /surf/lh.inflated files supposed to be produced when I follow the step described in the link? Or Is there any more step which is not written on the link? YUMI

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Left Right reversal
by Yumi Maeda 09 Jul '10

09 Jul '10

Hi, I am trying to do left right reversal of surface with the instruction of this link below. http://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal?highlight=(rever… After recon-all -subcortseg -s LRflipped-subject, I tried to see the result with this command , 'tksurfer LRflipped-subject hemi inflated'. There is this error message, MRISread(/////freesurfer//LRflipped-subject/surf/lh.inflated): could not open file No such file or directory tksurfer.bin: could not read surface file /////freesurfer//LRflipped-subject/surf/lh.inflated. No such file or directory How can I get surf/lh.inflated ? Is there any step that was not written on this instruction? YUMI

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Freesurfer July 2010