Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

mapping extracted MNI152 ROIs to individual subjects
by Paul Beach 13 Sep '13

13 Sep '13

Hello Freesurfer experts, I am currently trying to take extracted cortical networks from the Yeo_JNeurophysiol11_MNI152 package<https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011>and translate them to individual subjects to perform functional connectivity analyses - based on the individual networks, themselves. Currently the extracted ROIs are in '.nii.gz' format. My question is: How do I take the extracted ROIs and map them on to individual subjects? My thought was that mri_vol2vol could perhaps accomplish this, but I cannot find a help file for this command that would guide me in developing the line of code to write. Thanks! -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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Tracula and Qdec
by Alan Francis 13 Sep '13

13 Sep '13

Hi Anastasia and FreeSurfers: Is it possible to model Tracula data on Qdec? I have some interesting findings in FA and AD between two groups that I am hoping to visually represent on a single brain. Any advice would be deeply appreciated. thank you, Alan

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crash during longitudinal process when it run mri_ca_register
by Knut J Bjuland 13 Sep '13

13 Sep '13

Hi, I have run recon-al longitudinal process on abel cluster with this command recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all -debug. However, it crashed or is killed when it ran mri_ca_register. I have looked through the log, and I have not found a reason for it being killed even tough I added -debug. The cluster is running sbatch and CentOS release 6.4. Are there any debug options I can add or are there any debugversion of mri_ca_register I can download? This happen every time I run the program. I have asked for 8g ram when ran the program. Best regards Knut Jørgen Bjuland

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Re: [Freesurfer] license error with FS5.3
by S.V.Shepherd [work] 13 Sep '13

13 Sep '13

Solved: The license file actually differed from the other installations in that the "#----cut here-----" lines were included. To my embarrassment, it took a second pair of eyes to notice this. I thought I'd fess up lest anyone else make the same mistake. stephen

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Re: [Freesurfer] recon all question
by Rashmi Singh 13 Sep '13

13 Sep '13

Hey Bruce, I have two more questions. 1) I was suggested to use mri_binarize with brain.mgz to get the total brain volume. Is there any reference that I can cite regarding use of mri_binarize to calculate total brain volume. 2)I learnt that using T2 weighted image along with T1 weighted image from the same scanning session generates a good contrast and gives better segmentation/parcellation outputs using FreeSurfer. May the FreeSurfer experts guide me through this. Thanks, Rashmi ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Thursday, September 12, 2013 5:27 PM To: Rashmi Singh Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all question Hi Rashmi putting them in the orig folder with those numbers will get recon-all to do motion correction and averaging. cheers Bruce On Thu, 12 Sep 2013, Rashmi Singh wrote: > > Hello Freesurfer experts, > I am doing volumetrics study. During the scan we get 2-3 mprage per > scan for a subject. > While running the FreeSurfer, if I want to use the three mprages for > that subject as an input file, may I just keep the three mgz files > (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple recon > all command :=Recon-all -s (subject file name) -all or do I need to have > some additional l flags so that recon all command will use the three T1 > images to get one output file? > Thanks, > Rashmi > > 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.

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R: Re: R: Re: mris_calc erroe in recon-all
by stdp82＠virgilio.it 12 Sep '13

12 Sep '13

OK. But, I have run a simple command (recon-all) for cortical parcellation. I have already used this command for other structural images.This is the image features:data_type FLOAT32dim1 212dim2 320dim3 320dim4 1datatype 16pixdim1 0.8000000119pixdim2 0.8000000119pixdim3 0.8000000119pixdim4 0.0109999999cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ Thanks, Stefano ----Messaggio originale---- Da: rudolph(a)nmr.mgh.harvard.edu Data: 12-set-2013 17.50 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] mris_calc erroe in recon-all The file 'lh.area' contains 126850 elements. The file 'lh.area.pial' contains 126355 elements. You cannot add them together since they have different sizes. On 9/12/13 11:14 , stdp82(a)virgilio.it wrote: > Thanks. > > These are the output > [iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_calc lh.area stats > Size [ 126850 ] > Min@(index) [ -0.322716 > (56402) ] > Max@(index) [ 12.367171 > (123284) ] > Mean [ 0.587518 ] > Std [ 0.402374 ] > Sum [ 74526.703125 ] > Prod [ 0.000000 ] > [iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_calc > lh.area.pial stats > Size [ 126355 ] > Min@(index) [ 0.000000 (97676) ] > Max@(index) [ 22.833410 > (119901) ] > Mean [ 0.785660 ] > Std [ 0.738523 ] > Sum [ 99272.054688 ] > Prod [ 0.000000 ] > > but I do not understand what's happen. > > Stefano > > ----Messaggio originale---- > Da: rudolph(a)nmr.mgh.harvard.edu > Data: 12-set-2013 14.49 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] mris_calc erroe in recon-all > > The error would indicate that the number of elements in 'lh.area' and > 'lh.area.pial' are not the same. You can check this also with mris_calc: > > mris_calc lh.area stats > > mris_calc lh.area.pial stats > > which will provide some basic statistical output, including the size > (i.e. number of elements) of each. The sizes have to match in order to > add. > > HTH > -=R > > On 9/12/13 02:56 , stdp82(a)virgilio.it wrote: > > Hi list, > > > > I have a problem during recon-all > > > > #@# Surf Volume lh Thu Sep 12 08:25:31 CEST 2013 > > /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/surf > > \n mris_calc -o lh.area.mid lh.area add lh.area.pial \n > > > > mris_calc: > > Sorry, but I seem to have encountered an error. > > While checking on input filetype sizes, > > I found a size mismatch, i.e. len(input1)!=len(input2) > > > > Darwin iMac-di-Stefano.local 12.4.0 Darwin Kernel Version 12.4.0: Wed > > May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 > > > > recon-all -s SUBJECTS_DIR exited with ERRORS at Thu Sep 12 08:25:31 > > CEST 2013 > > > > For more details, see the log file > > > /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > Thanks, > > > > > > > > Stefano > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > 149 (2301) 13th Street, Charlestown, MA 02129 USA > > > > 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. > > > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Customized design matrix
by ye tian 12 Sep '13

12 Sep '13

Dear freesurfers, One of my categorical factors have three levels, and I would like to specify my own design matrix. What is a command line argument that I can use? Thank you very much! Sincerely, Ye

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recon all question
by Rashmi Singh 12 Sep '13

12 Sep '13

Hello Freesurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages for that subject as an input file, may I just keep the three mgz files (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple recon all command :=Recon-all -s (subject file name) -all or do I need to have some additional l flags so that recon all command will use the three T1 images to get one output file? Thanks, Rashmi

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old colin27
by Rouhollah Abdollahi 12 Sep '13

12 Sep '13

Dear freesurfer I am looking for old segmentation of Colin27 that you have replaced with new version. Is there anywhere that I can find archive of colin27 segmentations. I think it might be segmented with freesurfer 3 or 4. Because I have some labels from the old version. But I dont have the segmentation files and all surfaces. I think I need all surfaces to be able to use label2label command. one surface that I have, shows the lh.pial has 170783 vertices and it could be created in 2010 or before. Could you help me about that? -- Best Regards Rouhollah Abdollahi

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z-scores versus raw_age for correction in GLM_FIT or qdec
by Erik Lindberg 12 Sep '13

12 Sep '13

Dear Douglas, attached you´ll find the two y.fsgd file from the analysis run in GLM_FIT. the results are completely different (the z-score converted age produces a believable result, while the result correcting with raw age scores seems completely wrong. best regards Olof

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Freesurfer September 2013