Freesurfer

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11 participants
30080 discussions

Hi and for transfer AFNI data to Free Surfer
by Zhang, Xiaochu (NIH/NIDA) [F] 14 Nov '08

14 Nov '08

Hi FreeSurfer experts, I am a beginner of free surfer. Now I am working on my previous dataset with new hypothesis. In this dataset, I found a ROI (located almost in gray matter) showed significant functional difference between groups. I want to test whether the cortical thickness is changed or not in this ROI. I have done "recon-all -autorecon-all" and did some necessary check for data quality. However, I met some problems: 1. The ROI dataset was from AFNI. How will I transfer into free surfer? Which command I can use? 2. After ROI transfered, what will I do to get the averaged cortical thickness from this ROI? Are there some example or manual I can read and learn? Thanks a lot! All the best, Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619

2 1

longitudinal processing
by Jared Price 14 Nov '08

14 Nov '08

Hi everybody, 2 quick questions about longitudinal processing. 1) does the longitudinal processing even call the default gca atlas or does it use something else? 2) when processing say 7 time points should all longitudinal scans be processed from baseline or should time 3 be processed from time 2 etc.

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Re: Atlas
by sameer kumar 14 Nov '08

14 Nov '08

Hi all, I am trying to find the sub directory in the Freesurfer directory which contains all the atlases like MNI, JHU, etc. Can you please help me out... Thanks, Regards, Sameer Kumar Gottipati

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Creating a FreeSurfer label/volume
by joel bruss 14 Nov '08

14 Nov '08

Hello- I'm running freesurfer-Linux-centos4-stable-pub-v4.0.5 on Suse 11. I've used the output of FreeSurfer, specifically wmparc.mgz to create a 32-bit volume to which I've applied edits. The two commands I used were: mri_vol2vol --mov mri/wmparc.mgz --targ mri/rawavg.mgz --o wmparc-in-native.mgz --regheader --interp nearest mri_convert --in_type mgz --out_type analyze wmparc-in-native.mgz wmparc_in_native_analyze (The new Analzye set was renamed FSParcel.hdr/img) After making the appropriate edits, I wanted to put this file back into mgz format/freesurfer space so I ran: mri_convert --in_type analyze --out_type mgz FSParcel 3065_FSParcel.mgz mri_vol2vol --mov FSParcel.mgz --targ mri/wmparc.mgz --o FSParcel_FSorient.mgz --regheader --interp nearest (I assumed that a target of wmparc would be most appropriate sinc that's what I started with but I've tried aseg as well) I've been playing around with Slicer and trying load the file as a label file to which I create (I believe) vtk models. If I convert wmparc to an Analyze set and then back to FreeSurfer mgz without any edits, I get an exact copy, as would be expected. If I make any alterations to the file and follow my steps, Slicer gripes that it can't parse the header. No matter what dims I use, I get pixels scattered across the screen and it appears that the volume is scrunched to 1 slice. If I run tkregister (as mri_vol2vol suggests) tkregister2 --mov FSParcel_FSorient.mgz --targ $SUBJECTS_DIR/sub1/mri/aseg.mgz --reg FSParcel_FSorient.mgz.reg everything looks fine. I find the Slicer documentation a bit lacking and don't know who to turn to. Is there something inherently wrong with my commands or is there a way to write header params to the mgz file so that Slicer will just work? -Joel

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X Coordinates signs switched after Qdec
by Alexandru Hanganu 14 Nov '08

14 Nov '08

Dear Freesurfer users, We have made an analysis of 2 groups (i.e. patients, healthy subjects) in order to see the cortical thickness differencies. We have introduced these groups into Qdec. The results showed p-values on a scale from -5 to +5 and the X coordinates of the right hemisphere were negative. Two questions: - are the p-values actually t-values ? - normally the X coordinates of the right hemisphere should be positive. Any ideas why they are negative ? Thank's a lot for any help. Best regards, Dr. Alexandru Hanganu ___________________________________ Department of Neurology, Schleswig-Holstein University Hospital, Kiel Campus Arnold-Heller-Str. 3, building no. 41 D-24105 Kiel, Germany.

2 1

mri_convert
by Alexa Nardelli 14 Nov '08

14 Nov '08

Hi, I have a question regarding converting files to mgz format from siemens (dicom). Per each image I have 144 IMA files (i.e. for one subject I have files from .001.IMA to .144.IMA) and I am wondering how to convert those into 1 mgz file. The only way I seem to find is to use the command: mri_convert filename.001.ima subjectname/mri/orig/001.mgz mri_convert filename.002.ima subjectname/mri/orig/002.mgz ... mri_convert filename.144.ima subjectname/mri/orig/144.mgz While this is painful and time consuming I also worry that in my quest to find the hippocampal volumes, Freesurfer will not read these files as one volume. Is this the correct way to convert these files? Or is there another easier way? Thanks Alexa

2 1

for cortical thickness
by Zhang, Xiaochu (NIH/NIDA) [F] 14 Nov '08

14 Nov '08

Hi FreeSurfer Expert, Can I transfer the thickness data into other form, for example, Nifti, AFNI or SPM? Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619

2 2

Re: Atlases
by sameer kumar 14 Nov '08

14 Nov '08

Hi all, I am trying to find the atlases in the freesurfer directory. I could not find the specific atlases sub directory. Is there a sub directory that contains all the atlases like the MNI, JHU, etc? Regards, Sameer Kumar Gottipati

1 0

volumes of a 2 mm scan and a global thickness measure.
by asaf achiron 14 Nov '08

14 Nov '08

dear group, we acquired a scan of 2 mm. I know we cannot use FREESURFER to measure cortical thickness. however, can we use it to measure all the volumes like the Thalamus, Hippocampus, Amygdala etc.. in addition, in other scan of 1x1x1 we would like to know the whole cortex thickness and the thickness in each lobe, because in the aparc.stats we get for specific region. thank you Asaf

2 1

tksurfer ftimepoint variable
by Yigal Agam 14 Nov '08

14 Nov '08

Hi, I'm trying to use a TCL script that runs through every time point in a surface. I'm using the following commands: set gaLinkedVars(ftimepoint) 0 (or 1, 2, etc) SendLinkedVarGroup overlay But tksurfer is always showing point 0 (doesn't advance in time). Similar TCL commands for fthresh and fslope work fine. Any ideas?

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