Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

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by Nagy Szilvia 26 Oct '14

26 Oct '14

Dear Freesurfers, I would interest about when will the freesurfer course takes place in 2015? I realy need this info due to a travel grant deadline. Thanks, Szilvia Nagy

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Re: [Freesurfer] Changing subject names after processing
by Martin Reuter 26 Oct '14

26 Oct '14

One possible solution: Rename the time point in cross, in the base txt file (directly under the base directory, something with tps in it), in the base/mri/transforms/* files and in the long directory names and long/mri/transform files. I think these are all the places where subject names are stored, but no guarantee. Best Martin Sent via my smartphone, please excuse brevity. <div>-------- Original message --------</div><div>From: Janosch Linkersdörfer <linkersdoerfer(a)gmail.com> </div><div>Date:10/26/2014 6:05 PM (GMT-05:00) </div><div>To: mreuter(a)nmr.mgh.harvard.edu </div><div>Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> </div><div>Subject: Re: [Freesurfer] Changing subject names after processing </div><div> </div>Hi Martin and Doug, thanks for your answers! >>> theoretically it would be sufficient to rename the longitudinal directories accordingly as the base should not change at all, only some of the filenames -- not tested! Did I understand it correctly that if one has gone through the whole longitudinal processing stream (including corrections etc.), could one not remove the crosses and the base and just rename the longs to the new name as any further processing/stats is carried out only with them? Thanks, Janosch

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Re: [Freesurfer] Changing subject names after processing
by Martin Reuter 26 Oct '14

26 Oct '14

Hi Janosch, You could do that, but no further processing will be possible. The long runs take the asegs from the cross sectional runs and many other results from the base. Without base and long they can probably be used for statistical analysis (the roi stuff should work , for surfaces the base may be necessary). So in short it will create a mess. Some things may still work others not. Martin Sent via my smartphone, please excuse brevity. <div>-------- Original message --------</div><div>From: Janosch Linkersdörfer <linkersdoerfer(a)gmail.com> </div><div>Date:10/26/2014 6:05 PM (GMT-05:00) </div><div>To: mreuter(a)nmr.mgh.harvard.edu </div><div>Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> </div><div>Subject: Re: [Freesurfer] Changing subject names after processing </div><div> </div>Hi Martin and Doug, thanks for your answers! >>> theoretically it would be sufficient to rename the longitudinal directories accordingly as the base should not change at all, only some of the filenames -- not tested! Did I understand it correctly that if one has gone through the whole longitudinal processing stream (including corrections etc.), could one not remove the crosses and the base and just rename the longs to the new name as any further processing/stats is carried out only with them? Thanks, Janosch

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Re: [Freesurfer] Changing subject names after processing
by Janosch Linkersdörfer 26 Oct '14

26 Oct '14

Hi Martin and Doug, thanks for your answers! >>> theoretically it would be sufficient to rename the longitudinal directories accordingly as the base should not change at all, only some of the filenames -- not tested! Did I understand it correctly that if one has gone through the whole longitudinal processing stream (including corrections etc.), could one not remove the crosses and the base and just rename the longs to the new name as any further processing/stats is carried out only with them? Thanks, Janosch

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Freesurfer course 2015 Brazil
by Andrea Horváth 26 Oct '14

26 Oct '14

Dear Freesurfers, Does anyone know the exact date of the upcoming Freesurfer course in Sao Paolo, Brazil? I know that it is too early, but we need the date for a travel grant application. Thank you for your help in advance! Cheers, Andrea -- *Andrea Horvath M.D.* PhD Fellow Diagnostic Centre of Pécs horvath.andrea3(a)pte.hu

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smoothed outer pial surface for fsaverage
by Pierre Mégevand 26 Oct '14

26 Oct '14

Dear all, I'm trying to create smoothed outer pial surfaces for the fsaverage brain. I've tried simply using the following command: recon-all -s fsaverage -localGI But the resulting lh.pial-outer-smoothed doesn't look good (cf. attached screenshots). Do you have clues as to what did not work, or else has anyone already generated ?h.pial-outer-smoothed for fsaverage and would agree to share them? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Community <http://neuro.plos.org> editor - Follow us on Twitter <http://twitter.com/PLOSNeuro> Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter <http://twitter.com/pierre_vanmedge> - Read my blog here <http://neuroscimed.wordpress.com>

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virtual machine Linux with freesurfer, fsl and matlab
by elahe' yargholi 25 Oct '14

25 Oct '14

Dears, I need a virtual machine Linux with freesurfer, fsl and matlab installed on that, since I faced problem with software installed by myself. Do you know any site to download that? I do appreciate your attention. BR, Elahe'

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inf-lat-vent
by Mahmoudi, Fariborz 24 Oct '14

24 Oct '14

Hi all, Who knows what is exactly meaning of "inf-lat-vent"? Thanks, Fari

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Changing subject names after processing
by Janosch Linkersdörfer 24 Oct '14

24 Oct '14

Hi all, I wonder whether I can rename subjects after processing has been done and do further processing or stats on them without running in any problems. >From reading http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg26244.html, it seems as if the name of the subject folder under which everything else resides is the only marker and renaming it should be sufficient. But it seems the subject name is written in other places (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19285.html) Is this only a problem for de-identification or could it also cause other problems if the subject folder name and the name that is used elsewhere in the tree don't match. Are there special considerations regarding the longitudinal workflow? Thanks, Janosch

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How to overlay Freesurfer and FSL outputs
by Mahmoud 24 Oct '14

24 Oct '14

Dear all, I have a set of T1-MPRAGE images and and conducted the following steps: 1- Converted the DICOM images to SPM8 (3D nifti nii) by dcm2niigui.exe 2- Used the following line to segment images by FreeSurfer: recon-all -i /xxx/IM-0009-0001.dcm -subject TEST -all recon-all -base TESTBASE -tp TEST -all recon-all -long TEST TESTBASE -all 3- Used FSL BET to skull strip the nii file from step 1 and then fed the output into FSL FAST segmentation to segment it to 3 classes. 4- Used the following line to convert the mgz file to nii mri_convert --in_type mgz --out_type nii --out_orientation RAS /xxx/mri/brainmask.mgz /xxx/test_brainmask.nii 5- Using the fslinfo it gives me the following info for test_brain.nii.gz data_type FLOAT32 dim1 192 dim2 240 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ while for the nii file from step 4 the fslinfo gives me: data_type UINT8 dim1 256 dim2 256 dim3 256 dim4 1 datatype 2 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 2.300000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ As you may see these two files are completly different so I am not able to overlay them using FSLVIEW. Any idea about how to overlay them ? Thank you, Mahmoud

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