Freesurfer December 2012

freesurfer@nmr.mgh.harvard.edu

101 participants
161 discussions

Extracting resting state time series from surface space using Lausanne 2008 parcellation
by Chris McNorgan 04 Dec '12

04 Dec '12

Hi all. I have a question regarding the use of freesurfer + fs-fast preprocessing to apply the Lausanne 2008 parcellation scheme to some structural data, and then extract from those ~1000 ROIs the average time series from a 4D resting state functional run. I'm posting what I have carried out so far, both to verify that I haven't missed anything important, but also because I have seen evidence within this and other mailing lists that others are interested in doing something similar. This thread may then answer their questions as well. Structural and functional data is in $SUBJECTS_DIR/sub00?/mri and $FUNC_DIR/sub00?/rest, respectively For each subject: * I carried out recon-all -autorecon1, -autorecon2, -autorecon 3, checking data quality in between * inspected ?h.aparc.annot, possibly made minor edits ( https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit) * used cmtk.Parcellate() with the Lausanne 2008 scheme ( https://groups.google.com/forum/#!topic/cmtk-users/k_o3s8Yy2jQ) <https://groups.google.com/forum/#%21topic/cmtk-users/k_o3s8Yy2jQ> * This created a number of .label files and some .annot files, notably ?h.myaparcP*.annot, which have sub-parcellations of the 1-16, 17-28 and 29-36 regions indicated in the ?h.aparc.annot files (I'm not entirely clear why they couldn't just go into a single .annot file) * Converted the .annot files to surface space using mri_aparc2aseg --subXX --annot myaparcPXXXXXX which generated myaparcPXXXXX+aseg.mgz (3 files total, as each of three sets of lh and rh annot files describe both hemispheres in a single file) * ran each of the functional runs through: preproc-sess -s subXX -fsd rest -surface self lhrh -mni305 -fwhm 0 That brings me to my question. I have my functional data: $FUNC_DIR/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz (I also have 2 fmcpr.siemens.sm0.self.?h.nii.gz files, but they didn't work either) I want to pull the average timeseries data for the functional data out of the ROIs defined in myaparcP1_17+aseg.mgz (and similarly for the other two myaparcP*.mgz files) I tried mri_segstats \ --seg $SUBJECTS_DIR/subXX/mri/myaparcP1_16+aseg.mgz \ --i $FUNCTIONALS_DIR/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz \ --annot subXX lh lh.myaparcP1_16.annot \ --sum lh_1_16.sum.txt \ --avgwf lh_1_16.wav.txt However, this gave me the following output: sysname Linux hostname Sage machine x86_64 user chris Loading /home/chris/resting/anat/subXX/mri/myaparcP1_16+aseg.mgz Loading /home/chris/resting/func/subXX/rest/001/fmcpr.siemens.sm0.mni305.2mm.nii.gz ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 256 256 256 I then tried resampling my resting state data with mri_vol2vol using my func data as the --mov parameter, and my myaparc files as the --targ parameter, and used tkregister2 on the resampled volume. mri_segstats just hung when I ran it on the resampled volume; by the next morning nothing had been written to either text output file. I can open my ?h surface files in tksurfer, and then load in the appropriate timecourse ($FUNCTIONALS_DIR/subXX/rest/001/fmcpr.siemens.sm0.self.?h.nii.gz) and when I do so, I can click on various vertices and see timecourse plots. And I can paint my surfaces with .annot files that define my ROIs. So it seems I should be able to get these timecourse data from ROIs in surface space without making a thousand individual ROIs in volumetric space (my guess is I'd use flsmaths on my myaparc files to do this). But I am not clear if mri_segstats can be used in this way, or if indeed it is the appropriate tool. Any assistance to get me through this last step would be appreciated. Thanks

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wmparc 2 wmsurf
by Juranek, Jenifer 03 Dec '12

03 Dec '12

I'm running FSv5.1.0 on RHEL6. 1) My goal is to run a glm-fit on White Matter aparc regions for a "between group" surf-based analysis and evaluate spatial maps of significant differences. 2) I noticed that fsaverage does not have a wmparc.mgz file, so I'm currently working with bert as my subject. 3) I'd like to visualize each segid in the wmparc.mgz (volume-based) file on the white matter surface in the same subject (e.g. bert). 4) I have been able to breakdown bert's wmparc.mgz file into separate masks (e.g. *.mgz) and labels (e.g. *.label) based on segid using mri_cor2label and mri_vol2surf. To get the vertices written into the label file, I have loaded each label and re-saved each label in tksurfer. Q: Is there a better method for getting this (wmparc units moved from vol to surf) done (maybe using a matlab function?) Or is surf-based analysis of white matter not such a good idea. Many Thanks for any assistance you can provide. Cheers, Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Jenifer Juranek, PhD University of Texas at Houston

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Reducing pial and main surfaces
by Jonathan Holt 03 Dec '12

03 Dec '12

I have not seen a lot of documentation on how to do this. I've attached two images of specific areas where I'd like to have the pial and main surfaces follow the actual surface of the brain. The aux volume OK in both of these cases. The empty space is segmented as white matter. In the past I have tried deleting the segmentation values and saving the segmentation, then running recon-all -autorecon2 -autorecon3 -s <subjid>. Unfortunately it just resegmented the same areas as white matter and the issue was never resolved. I know about freeview but I do not know how to manually edit surfaces... What should I be doing here? jon

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Insula missing
by José Ángel Pineda 03 Dec '12

03 Dec '12

Dear experts, I am registering cortical labels from Talairach coordinates to my native T1. For doing this, I have run the next script lines: tkregister --targ brainmask.mgz --mov highres_brain.nii.gz --reg T1FS2Highres.dat --regheader --noedit mri_label2vol --annot rh.aparc.annot --temp highres_brain.nii.gz --reg T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject FS --proj frac 0 1 .1 --fillthresh .3 and the same for the left hemi. However I am finding two problems at the result. First Insula is missing for both hemispheres, and second the cortical ROIs have the shape of the figure attached, e.g. there are many voxels empty [image: Imágenes integradas 1] I found in previous topics, that the mri_label2vol, was updated as it left last volume from the list out of the conversion. I tried to download it, but it is just compiled for linux, and since Im working with mac I am not able to run it. Could you please give me any comments to solve the problem with the missing voxels. About the problem with the insula, the other option is to just extract it with mri_annotation2label, but if I could get the mri_label2vol working correctly it would be better. Thanks a lot Jose -- José Angel Pineda Pardo Center of Biomedical Technology (CTB) Parque Científico y Tecnológico de la UPM Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, ES

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hippocampal subfield segmentation
by Antonella Kis 03 Dec '12

03 Dec '12

Dear FS team, I would like to know if there is any options to get the hippocampal subfield segmentation so I can get the volume for each segmentation if I was running only recon-all for all my subjects or I need to re-run recon-all but with a hippocampal subfield segmentation option this time? Many thanks, Antonella

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missing brain
by Catherine Bois 03 Dec '12

03 Dec '12

Hi, I am currently in the process of reconstructing my brains after edits. However, the brains keep being reconstructed with large portions of brain missing/cerebellum missing; ie they are much worse than before I edited them. However, I am sure that I have only put control points in white matter areas; ie not partial volume, so I am very confused as to why this is happening; in one brain for example I had not put any cotnrol points (only made a very small white matter edit). Has this happened to anyone else before? Am i somehow running the wrong command somewhere? Could the watershed be wrong in the script, ie accidentally changed? Grateful for help, Regards Cathy

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aseg.stats
by charles laidi 03 Dec '12

03 Dec '12

Dear freesurfers. I'm using freesurfer for two weeks. I'm currently trying to make a script to get asegstats resultats for >100 patients. I did this script in tcsh : foreach filename (t1_????????) asegstats2table --subjects ${filename} \ --segno 12 18 14\ --tablefile asegstats.txt end The problem is that at each loop, the n+1 subject replace the n subject, so at the end I only have the asegstats for the last subject. When I am replacing t1_???????? (it's a wild card) by t1_63537193 t1_18394856 the result is fine so the question is : how to make a loop without over writing the n result by the n+1 result Thanks very much for you help Sincerely yours, Charles Laidi

2 1

freeview
by Yaniv Kaufman 03 Dec '12

03 Dec '12

Dear Freesurfer experts, I am trying to display DTI using freeview, however, every time I attempt to run freeview from the command line (I am using Ubuntu 12.4), I receive the following error: "freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory" libjpeg.sp.62 is present in /home/freesurfer, when I attempt to open it directly, it gives the following error: "The link cannot be used, because its target 'libjepg.so.8' doesn't exist" libjepg.so.8 does in fact exist but in /usr/lib. I am not quite sure how to direct libjpeg.so.62 to libjepg.so.8 or whether that would solve the problem at all. I am able to use tkmedit, tksurfer and do all the pre processing for MRI and DTI. Thank you in advance. Yaniv Kaufman

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Coregister a combination of T1, and Flair images ?
by Assaf B. Spanier 02 Dec '12

02 Dec '12

Hi@all, I have a dataset of several MRI T1 images and one Flair. All images of the same subject and were taken in the same session. My goal is to register and segment all those MRI images. *= A =* In my first try I have used, "recon-all -i image1 -i image2 etc'" for all T1 images (here, I didn't use the Flair images ) . Follow this, I used the " recon-all -all" command. (For about two days...) Here come Question 1: After all this process, I didn't completely follow the results I got... As I have noticed that I have only one segmentation file (aparc.a2009s+aseg.mgz) ? How can I see the segmentation result with tkmedit in the different brain images ? *= B =* As I would like the neuroanatomical labels to be inspected for accuracy by a physician. My physician asks to see the segmentation result on top of the Flair images (saying it easier for him to do so on Flair images) So I've used the "recon-all -i image1 -i image2 etc'" command again but this time I've also included the Flair image. Here come Question 2: However, this time, unfortunately, the "recon-all -iimage1 - i image2 etc'" , failed, saying that: ~~~~~ images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.5078, 0.5078, 5.5 size(0) = 0.51, 0.51, 5.5 ~~~~~ Is there something I can do to fix this ? Thanks for everyone involved in this great project! Highly appreciate your time and efforts. Best, Spanier

3 13

recon-all error
by aini ismafairus 01 Dec '12

01 Dec '12

Hello, I still new in using freesurfer. the freesurfer was successfully installed. but when i tried to run recon-all it give an error. [Ainis-iMac:~] ismafairus% setenv FREESURFER_HOME Applications/freesurfer [Ainis-iMac:~] ismafairus% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Applications/freesurfer FSFAST_HOME Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR Applications/freesurfer/subjects MNI_DIR Applications/freesurfer/mni FSL_DIR FSL/fsl Ainis-iMac:~] ismafairus% recon-all -i $SUBJECTS_DIR/us03.nii.gz -o us03 -all ERROR: cannot find Applications/freesurfer/subjects/us03.nii.gz Darwin Ainis-iMac.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Sat Dec 1 11:42:54 CET 2012 Advice on how to troubleshoot this would be appreciate. Thank you. Regards, Isma

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Freesurfer December 2012