Freesurfer

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30088 discussions

mri_volcluster register.dat question
by Huiting Liu 14 Feb '12

14 Feb '12

Hello all, I'm trying to run mri_volcluster on our third-level functional data and one of the required flagged arguments is the register.dat file. Our data preprocessing/registration was done in FSL, not Freesurfer, so we don't have this particular file. Is there anything we can do to get around this or do we need to run tkregister first in order to use mri_volcluster? Thanks for your time. -Huiting

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mri_vol2surf
by Klein, Holger 14 Feb '12

14 Feb '12

Dear FreeSurfers, To get a better view on the pial surface of the Heschl' Gyri I used the command mri_vol2surf after having created the suitable label with (label2vol). My goal is to get My Command was: *mri_vol2surf --src pf_lh_vol.mgz --hemi lh --srcreg register.dat --out_type paint --o A1surf-lh.w* The output file was created without any error, but loading the file in freeview or tksurfer an error occured: *command: tksurfer WH lh A1surf-lh.w * * * *subject is WH* *hemi is lh* *surface is A1surf-lh.w* *surfer: current subjects dir: /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide* *surfer: not in "scripts" dir ==> using cwd for session root* *surfer: session root data dir ($session) set to:* *surfer: /freesurfer/Kontrollen/A1_Wilts_Heide* *checking for nofix files in 'A1surf-lh.w'* *Reading image info (/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH)* *Reading /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* *surfer: Reading header info from /Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/mri/orig.mgz* *ERROR: MRISread: file '/Volumes/Macintosh/Freesurfer/Kontrollen/A1_Wilts_Heide/WH/surf/lh.A1surf-lh.w' has 0 vertices!* *Probably trying to use a scalar data file as a surface!* * * Any help would be greatly appreciated. Thanks in advance Holger

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Re: [Freesurfer] Clusters locations
by Douglas Greve 14 Feb '12

14 Feb '12

Hi Antonella, what level of detail do you want? I think that most people are reporting MNI coordinates. doug On 2/13/12 2:44 PM, Antonella Kis wrote: > Hi Doug, > > I will be very grateful if you give me some directions regarding how I > can get my clusters location ( my output is too general telling me > just Left-Cerebral-White-Matter and Right-Cerebral-White-Matter) and > the coordinates (MNI) when I run the: > > mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask > GroupAnalysis_pos.glmdir/mask.mgh --no-fixmni --cwsig > GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum > GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn > GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh > .09 --seg cvs_avg35 aseg.mgz --csdpdf > GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd > GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig > GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh > > and > > > mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i > /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.nii.gz > --avgwf fa.avg.dat --sum permcsd.sig.cluster.summary > > > Thank you. > Antonella

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reference for corpus callosum segmentation
by Kelsi Hirai 13 Feb '12

13 Feb '12

Hi freesurfers, We are using the segmentation of the corpus callosum into the Anterior, Mid Anterior, Central, Mid Posterior, and Posterior sections that are labeled in the freesurfer aparc+aseg file. However, some of the labeling is not correct in subjects post-stroke, so we need to manually draw some of the regions. What are the divisions based on? Is there a reference paper that describes the segmentation in more detail? Thank you! Kelsi

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RD radial diffusivity and AD axial diffusivity
by Antonella Kis 13 Feb '12

13 Feb '12

Dear All, I would like to know how I can get the RD radial diffusivity and AD axial diffusivity after I was running dt_recon. I can see my mean diffusivity adc.nii and a file called radialdiff.nii but I am not sure which one is the AD and Rd. Can you please tell me the name of this files AD and RD as an output from the dt_recon? Thank you. Antonella

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Question regading paired samples t-test
by Maren Strenziok 13 Feb '12

13 Feb '12

Hi, I want to set up a paired samples t-test to look at pre-post differences in cortical thickness in a group of subjects that underwent cognitive training. I could not get any information on this from the internet other then the suggestion to use the --paired -t flag. This, however, didn't work. I tried to build an fsgd file based on how I would set up the test in FSL, but that didn't work either. Any instructions on how to build the correct matrix and contrast files or an example would be highly appreciated. Thanks, Maren Maren Strenziok, Ph.D., Psychologische Psychotherapeutin (PTG) Postdoctoral Fellow, Arch Lab Department of Psychology 2071B David King Hall George Mason University MS 3F5, 4400 University Drive Fairfax, VA 22030-4444 Phone: 301-318-8912 Email: mstrenzi(a)gmu.edu

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mris_make_face_parcellation
by Franz Liem 13 Feb '12

13 Feb '12

Dear Freesurfers, I have some questions regarding mris_make_face_parcellation (and possibly found one error in the .tri file). (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0). I would like to make a high res parcellation of several subjects and used ic3.tri. Parcels should correspond across subjects. I computed mris_make_face_parcellation ../surf/lh.sphere $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot 1. It seems not to make a difference whether I choose .sphere or .sphere.reg as input, the resulting parcellations are identical (i checked by comparing vertex label values in matlab; .inflated deviates a bit, but not substantially). According to Bruce (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18509.html) "You want to use either ?h.sphere if you want it to be uniform in subject space or ?h.sphere.reg if you want the parcels to correspond across subjects" Could anybody tell me how the parcellation is performed exactly? I thought it was performed on the input surf (the input surf is parcellated into (e.g.) 642 equally sized parcels), which should lead to different results at .sphere and .sphere.reg, shouldn't it? Alternatively, would it be better to mris_make_face_parcellation the fsaverage and mri_surf2surf the high res parcellation onto each subject to get cross-subject correspondency (I tried this. It didn't look that great with this command: mri_surf2surf --srcsubject fsaverage --sval-annot ic3.annot --trgsubject subject1 --tval ic3s03.annot --hemi lh )? To recap, what is the best strategy to arrive with cross-subject-corresponing parcellations? Performing mris_make_face_parcellation with ?h.sphere.reg for each subject individually? 2. There seems to be duplicate structNames/annotationValues when applying mris_make_face_parcellation with ic3.tri In fsaverage at least the following labelnames are given to two spatially separated labels. ic3.tri_vertex_25 (cluster 1 around vertex 41132, cluster 2 around vertex 157199) ic3.tri_vertex_42 (cluster 1 around vertex 137845, cluster 2 around vertex 155417) How come? Thanks for you help, Franz

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make_average_volume error
by Martina Ly 13 Feb '12

13 Feb '12

Dear freesurfers, I am coming across an error in the beginning of make_average_volume of make_average_subject where mri_convert fails. make_average_surface finished without a problem so hopefully that part will not need to be re-run. I've check permissions, cpu space, paths but couldn't find anything... Any help/suggestions would greatly appreciated. Below is the error message: INFO: Applying transformation from file /study/NCCAM/Data/MRI/processed/structural/freesurfer//WB101_1//mri/transforms/talairach.xfm... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.156 0.062 0.028 -2.110; -0.102 1.113 0.318 -31.524; -0.029 -0.322 1.218 4.598; 0.000 0.000 0.000 1.000; INFO: Transform dst volume info is not used (valid flag = 0). INFO: assumes that the dst volume given is the same as the dst for the transform mghWrite(/study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_average_vol-tmp-2117/orig-WB101_1/.mgh, -1): could not open file --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_average_vol-tmp-2117/orig-WB101_1/.mgh... ERROR: failure writing /study/NCCAM/Data/MRI/processed/structural/freesurfer//average/tmp/make_average_vol-tmp-2117/orig-WB101_1/.mgh /study2/NCCAM/Data/MRI/processed/structural/freesurfer ERROR: mri_convert failed. Many thanks in advance, Martina

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Hippocampal subfield: average standard T1 ore use higher resolution
by Grimm, Oliver 12 Feb '12

12 Feb '12

Dear FreeSurfer-User, some of my questions are mentioned in some older postings, but I still struggle with some basic questions. We are planning to use the new hippocampal subfield segmentation of FS 5.1 with 3 T Siemens TRIO with 32 channel head coil. Still, I do not fully understand how to optimize our image processeing pipeline: 1. Freesurfer works internally with 1x1x1 mm3 but the hippocampal segmenat uses a higher res. of 0.5 x 0.5 x 0.5 mm3. So should we instead use a higher resolution for the hippocampal subfield seg.? 2. I understand that the recent FS version is not working well with high resolution images, e.g. the atlases are not provided in a higher res, however the hippocampal subfield segmentation seems to make use of aseg.stats. So is is possible at all to use the FS-pipleine in this case (hippocampal subfields)? 3. Instead of using a high resolution image, we could average over several pictures. When I tried this, I had the visual impression, that there was almost no gain in this, the volume estimates were bouncing within a range of 10% but did not converge when averaging from scan 1-5 to a specific value. So is it necessary for a good quality to average images when using hippocampal subfield segmentation ? Thanks for your efforts! Best, Dr. med. Oliver Grimm Zentralinstitut für Seelische Gesundheit www.zi-mannheim.de SNiP | Systems Neuroscience in Psychiatry 68159 Mannheim Germany Tel: +49-621-1703-6341 Fax: +49-621-1703-6305 email oliver.grimm(a)zi-mannheim.de <mailto:oliver.grimm@zi-mannheim.de>

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Hippocampal-subfields to ROI
by Joshua Lee 12 Feb '12

12 Feb '12

Hi All, I am wanting to run a functional analysis in spm using the hippo-subfields as individual roi's. Thus I need to convert into a binary mask that is in SPM space. Knowing that the sub-field segmentations are probabilities [0..255] I chose a threshold (i.e. ~95% certainty, corresponding to a value of ~240) and ran mri_binarize with a min set at 240. However, the resultant image doesn't retain the same dimensions as say brain.mgz, and appears as a black square when overlayed. I suspect this will not work as a mask for roi analysis. Any suggestions? Thanks Josh

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