Freesurfer

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30132 discussions

-clean
by Joshua Lee 20 Apr '12

20 Apr '12

If I were to want to re-run a recon-all completely fresh on a subject, what do I need to do aside from creating a new subject directory? I had previously thought that by adding the -all flag, all old files would be over written (i.e. overwrite with a new brainmask.mgz). I want everything fresh. Does the -clean flag do it all? Thanks Josh

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Brainmask.nii Reading
by Nooshin Zadeh 20 Apr '12

20 Apr '12

Dear FS friends I need to do skull stripping of MRI images, and for this purpose I have used FS. For reading the data from "brainmask.mgz", I converted it to "brainmask.nii". Can you please tell me how can I read the data from "brainmask.nii" is MATLAB? Do you know other way of reading the data from brainmask.mgz? I am looking forward to hear from you. Thanks in advance -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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long_qdec_table error
by Derin J Cobia 20 Apr '12

20 Apr '12

Martin, I'm getting the following error when running long_qdec_table: ========= [derin@otis ccnm_mprage_v4.5_long]$ long_qdec_table --qdec qdec/ccnm_prog_30_long_Th.qdec.table.dat --cross --out qdec/ccnm_prog_30_long_Th.cross.qdec.table.dat Parsing the qdec table: qdec/ccnm_prog_30_long_Th.qdec.table.dat Traceback (most recent call last): File "/pkg/brainmap/freesurfer-v5.1.0/bin/long_qdec_table", line 142, in ? longqdec = LongQdecTable(options.qdec) File "/pkg/brainmap/freesurfer-v5.1.0/bin/LongQdecTable.py", line 30, in __init__ self.parse(stpmap) File "/pkg/brainmap/freesurfer-v5.1.0/bin/LongQdecTable.py", line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range ========= I haven't had much luck troubleshooting it, maybe I have too many numerical variables in the table? I guess I could always reconstruct it by hand, but wondering if you had any thoughts, thanks. FS v5.1.0 CentOS 4 -Derin

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Re: [Freesurfer] WM modification
by Gabriel Gonzalez Escamilla 20 Apr '12

20 Apr '12

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How to switch order of Talairach and nu-correction stages in recon-all
by Ed Gronenschild 20 Apr '12

20 Apr '12

Hi, As of version 5.1 the Talairach stage precedes the nu-correction stage. Is there an option or possibility to switch this order? Cheers, Ed

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Re: [Freesurfer] bbregister for fmri FEAT data
by Erlend Hodneland 20 Apr '12

20 Apr '12

Hi again, (This mail is a response to the communication below from the FreeSurfer list, Friday 13 April 2012 09:16:36 -0700). The registration looks fine in tkregister2, but is apparently wrong in fslview (and also mricron). See the attached files showing screenshots of fslview and tkregister2. How can this be explained, and how can we visualize the correct orientation in fslview? What does this misalignment influence any further processing with fnirt and concatenation of the affine transformation fields? This is our command we run for bbregister: bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat --init-fsl --t2 --o test.nii.gz where vol0001 is the first volume in the fmri sequence and is flipped to align with LAS (as the highres). Thank you for your kind help, Erlend Hodneland Re: [Freesurfer] bbregister for fmri FEAT data Douglas N Greve Fri, 13 Apr 2012 09:16:36 -0700 what do you mean that it is in the wrong orientation? It should be in the same orientation as the anatomical. How does the reg look in tkregister2? Note that fslview can display volumes in odd orientations even when the orientation is correct. doug On 04/13/2012 03:31 AM, Erlend Hodneland wrote: > Hi, > > we are trying to register fmri FEAT data (example_func.nii) to the > anatomical scan (processed in Freesurfer) using bbregister to opt. > the affine registration before running FNIRT. > > However, the orientation of the registered image is flipped around and > is incorrect after applying bbregister. > > We have tried: > > 1) bbregister --s subj_501 --mov example_func.nii.gz --reg > register.dat --init-header --bold --o example_func2highres-fs.nii > 2) bbregister --s subj_501 --mov example_func.nii.gz --reg > register.dat --init-fsl --bold --o example_func2highres-fs.nii > 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat > "myfeatdirectory" > 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat > (this one looks correct) > followed by > bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat > --init-reg tkreg.dat --bold --o example_func2highres-fs.nii > > 5) reorienting to match the highres: > > fslorient -swaporient example_func > fslswapdim example_func x -y z example_func_swap (correct > orientation) > > followed by > bbregister --s subj_501 --mov example_func_swap.nii.gz --reg > register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii > > with the output being flipped in wrong orientation for all options. > > We would greatly appreciate if you have any suggestions for how to > overcome this problem! > > Cheers/Sincerly/All best > > Erlend Hodneland > > > > > _______________________________________________ > 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 Centergr...(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 _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://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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Re: [Freesurfer] TRacula and Philips
by Anastasia Yendiki 20 Apr '12

20 Apr '12

Hi Fabricio - You can only use the formats supported by mri_convert: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert Dicom or nifti is recommended. Hope this helps, Anastasia. On Thu, 19 Apr 2012, fabricio feltrin wrote: > Hi Anastatia. > Is it possible to use REC/PAR images from philips in tracula? > > Thanks. > Fabrício. > >

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-use-mritotal
by Steven Korycinski 19 Apr '12

19 Apr '12

Hi all, I've been following an e-mail on this list-serve from Joshua Lee regarding poor hippocampal segmentations in Freesurfer 5.1. He mentions "using -use-mritotal in the recon-all command to overcome tal-check failures" to help fix the segmentation and make them more like "those produced by Freesurfer version 4.xx." In light of this information, would you recommend that all normal Freesurfer 5.1 users add this flag to the recon-all command to help with any segmentation errors? Also, at what stage(s) in the reconstruction process should the flag be included (ie. recon-all -autorecon1,2, or 3)? Thanks, Steve

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what is mri_cvs_register.settings.txt?
by Jackie Leung 19 Apr '12

19 Apr '12

Hi, I'm new to Freesurfer, so this may be a silly question. I would like to run mri_cvs_register, but I decided to run mri_cvs_check first to make sure I have all the files. This is the message I received: FreeSurfer:/mridata/fs_analysis> mri_cvs_check --mov sub26 --template sub47 The following files are missing: /home/virtualuser/freesurfer/bin/mri_cvs_register.settings.txt You need to find these files or run reconall on the data in order to run mri_cvs_register. Does anyone know what this mri_cvs_register.settings.txt is? I doubt running reconall will help. thanks, jackie

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Re: [Freesurfer] Question about FreeSurfer
by Martin Reuter 19 Apr '12

19 Apr '12

Hi Kourosh, you can ask the freesurfer list for these kind of questions. I believe that the ras coordinates are not changed, so reslicing everyhting as the original inputs will be sufficient (no transform, only based on the header information) e.g. mri_convert -rt nearest -rl youroriginialinput.mgz labels.mgz labelsinorig.mgz if it is labels (e.g. aseg.mgz) you are mapping, use nearest neighbor, else use -rt cubic (in the dev version) in stable versions (5.1 and earlier) just stick with linear (default). Best, Martin ----- Original Message ----- From: "Kourosh Jafari-Khouzani" <kjafari(a)nmr.mgh.harvard.edu> To: "Martin Reuter" <mreuter(a)nmr.mgh.harvard.edu> Sent: Thursday, April 19, 2012 10:04 AM Subject: Question about FreeSurfer > Hi Martin, > > I have a question about FreeSurfer subcortical segmentation: FreeSurfer > reslices an image and makes the voxel 1 mm isotropic and then segments it. > Is there a command to map the labels back to the original image? > > In case you don't know the answer, do you know anyone who may know it? > > Thanks! > Kourosh > > >

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