Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

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.

2 3

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

3 3

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

2 4

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

2 1

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

1 0

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

2 1

Interpretation of red/blue clusters in group analysis
by Anita van Loenhoud 12 Sep '13

12 Sep '13

Hi FreeSurfers, I'm doing an analysis with two groups: patients and controls. When I look at "Does the average thickness differ between 1 (patients) and 2 (controls)?", I can see blue (negative) and red (positive) correlations. I know that it means that in some cases, the patients have a higher cortical thickness compared to the controls, and in others it's the other way around. But which is which? Since most of the clusters are blue, I assume that blue means: patients have a lower cortical thickness compared to controls, and red means: patients have a higher cortical thickness compared to controls. Is this correct? How does FreeSurfer decide which group to use as the 'reference group' (i.e. the group to which the other group is compared)? Thanks, Anita

2 1

talairach transforms
by swathy p.s 12 Sep '13

12 Sep '13

after motiioncor was runned sucessfully,getting error with talairach.comand was as given bellow [root@ml freesurfer]# recon-all -talairach -subjid Stress_v12 Terminal window display was as shown bellow Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r--. 1 root root 346264 Sep 10 23:10 /usr/local/freesurfer/subjects/Stress_v12/scripts/recon-all.log Linux ml 3.3.4-5.fc17.i686 #1 SMP Mon May 7 17:45:26 UTC 2012 i686 i686 i386 GNU/Linux nu_correct: Command not found. #-------------------------------------------- #@# Talairach Tue Sep 10 23:11:50 EDT 2013 /usr/local/freesurfer/subjects/Stress_v12/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux ml 3.3.4-5.fc17.i686 #1 SMP Mon May 7 17:45:26 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s Stress_v12 exited with ERRORS at Tue Sep 10 23:11:55 EDT 2013

2 2

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

12 Sep '13

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.

2 1

Watershed and Normalization Problem
by Erica Tatham 12 Sep '13

12 Sep '13

Hello Freesurfer People, Below is the error that I have been receiving after running a recon-all. There seems to be a problem in the normalization stage. I checked the orig.mgz and the transform.xfm, and both seem to be reasonable. I was hoping for some guidance/expert advice for how to precede from here. I have not tried to add control points as I am fairly novice to freesurfer and not quite sure how to complete this task. Thank you for any advise you are able to give, Cheers, Erica Error: *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all.

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer