Freesurfer November 2014

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

mri_watershed -brain_atlas undocumented?
by tvg[fs] 04 Nov '14

04 Nov '14

- This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for "-atlas"? Does the "-brain_atlas" flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 $ mri_watershed --version stable5

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mri_label2label
by Roberta Santoro 04 Nov '14

04 Nov '14

Dear all, I would like to draw a ROI on a group average surface (template) and map it back to the surface of individual subjects. For this, I would like to create the template based on my subjects, rather than using fsaverage. As far as I understood, I should first create the template by using: make_average_subject –out myAvg –subjects s1 s2 … Then, I should register each subject to the template with: mris_register --curv s1/surf/lh.sphere SUBJECTS_DIR/myAvg/lh.reg.template.tif s1/surf/lh.sphere.reg.myAvg. At this point, I can map the ROI to a given subject by using the command mri_label2label: mri_label2label --srclabel labelName --srcsubject myAvg --trgsubject s1 trglabel OutputLabelName --hemi lh --regmethod surface. There is one thing I don’t understand: how can I tell the command mri_label2label that it should use the registration file that I have created in the previous step (namely lh.sphere.reg.myAvg)? If I don't specify anything, is the function going to use the sphere.reg file that refers to the registration between subject s1 and fsaverage? In general, is the pipeline I described correct? Thanks a lot for your help. Best Roberta

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Quality of surface-based alignment
by Caspar M. Schwiedrzik 04 Nov '14

04 Nov '14

Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar

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Fsaverage for ROI analysis of children
by Smith, Michael 04 Nov '14

04 Nov '14

Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 Best, Michael S.

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Re: [Freesurfer] Before recon-all, is it necessary to set origin of the image?
by Bruce Fischl 04 Nov '14

04 Nov '14

Hi Ngoaka no, you don't need to set the origin of the image. Just point recon-all at a single slice from the correct dicom series (of a highres T1-weighted scan) with the -i <full path and file name of dicom slice> -all -s <subject id that you pick> and you should be good to go cheers Bruce On Tue, 4 Nov 2014, CHONNIKAN JONGKREANGKRAI wrote: > > Dear all, > > > I'm new on FreeSurfer. > I want to calculate cortical thickness, hippocampus volume from MRI images > (obtained from ADNI). > > After installation, I tried recon-all. >> Only this process, can I obtain > cortical thickness and hippocampus volume? > > And someone told me that I have to set origin of the image of each case > using SPM program. > > I want to know that is it necessary? > > > Thank you for your kind attention > > > Best Regards, > > Ngoak > > > >

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longitudinal data processing
by Robby De Pauw 04 Nov '14

04 Nov '14

Dear FS-experts Is there any command that I can use for caching my preprocessed data in the recon-all longitudinal stream, since this is possible through adding the -qcache option in the cross-sectional pipeline. Or maybe this is already automatically done without adding any option to the command? Thank you Greeting Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be

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Fwd: Underinclusion of Gray Matter
by Christina Chen 04 Nov '14

04 Nov '14

Hi, Are there any ways to fix underinclusion of gray matter cortical edges when the white matter is fine? Attached is a picture. Thanks, Christina

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permission denied
by Ali Radaideh 04 Nov '14

04 Nov '14

Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. Thanks in advance, Ali -- *Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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mri_watershed -brain_atlas undocumented?
by tvg[fs] 03 Nov '14

03 Nov '14

Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for "-atlas". Does the "-brain_atlas" flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 > mri_watershed --version stable5

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registering coronal images
by Mahmoud 03 Nov '14

03 Nov '14

Dear all, I have some T1 images which are originally in coronal view and the in-plane resolution is 0.5x0.5mm and slice thickness is 2mm. The matrix size is 512x512. I need to segment the left and right hemisphers. As the head is tilted I also need to register the images. Which atlas you recommend to use for this case ? Does MIN152_T1_0.5mm work better or MIN152_T1_2mm ? Thank you, Mahmoud

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Freesurfer November 2014