Freesurfer March 2011

freesurfer@nmr.mgh.harvard.edu

111 participants
170 discussions

reg-feat2anat problem
by Cris Lanting 29 Mar '11

29 Mar '11

Dear all, I'm having a slight problem with reg-feat2anat to transform functional data (FSL) to anatomical (Freesurfer) in that the resulting transformation seems completely wrong. What I've done so far is the following: 1) run FEAT including the normal FEAT registration (which I know fails due to a lack of FOV in the functional data) 2) re-run the Flirt for a proper registration (i.e. by using the -usesqform option to obtain better registration) 3) overwrite the example_func2highres.mat, highres2standard.mat and example_func2standard.mat file with the newly obtained registration files. (The resulting files are now properly registered when viewing in e.g. fslview) 4) Run updatefeatreg <featdir.feat> 5) Start FEAT and change the mode to run Post-stats only. Select the FEAT output directory as input. Go into the registration tab and turn off all registration. Press GO. (steps 3-5 following the FSL FAQ on custom registration into a FEAT analysis) 6) run a complete freesurfer segmentation and all the rest using recon-all etc 7) reg-feat2anat --feat featdir.feat --subject subjectid When I now check the registration, it seems completely wrong... My guess would be that it has to do with the re-registration in steps 2-5 but as far as I can tell the files are registered properly to the anatomy scan (and to the template (or standard), the MNI152_T1_1mm_brain file) Any ideas? (Not sure whether it is appreciated if I send a screenshot as attachment, so I'll leave it for now) Cheers, Cris

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problems with set gaLinkedVars(vertexset)
by Iris.Steinmann＠uni-heidelberg.de 29 Mar '11

29 Mar '11

Hello Freesurfers, I have a little problem using a tcl script with tksurfer. I want to load the pial surface to a cuted patch. So I used the following comandline: tksurfer fsaverage lh inflated -patch testpatch -tcl test.tcl test.tcl include the following lines: set gaLinkedVars(vertexset) 3 SendLinkedVarGroup view redraw but nothing happend! Surprisingly, after running the tcl script, in the 'TkSurfer Tools' window the button with the pial-brain looked like pressed. But the pial surface is not loaded. I would be very thankful for a solution. Iris

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Re: [Freesurfer] Problem with Freesurfer
by Marie ERESUE 29 Mar '11

29 Mar '11

Hi Bruce, > thanks for your answer. In fact, I wrote: > -recon-all -i home/pmod/Bureau/freesurfer/subjects/Marie/image(n).nii -subjid image(n) > in order to analyse my images. I created folders for each patient, but when I try to open these (tkmedit) I can't recover ... I have new folders (bem, label, mri...), and 001.mgz into mri folder, but I can't open it. > > My goal is to register SPECT with MNI152_T1_2mm_brain, with CT and IRM like intermediate step. Is it possible? I'd like to compare like this my work with FSL (flirt and fnirt) and freesurfer. > > Best regards, > > Marie

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[Re] Problem with freesurfer
by Marie ERESUE 29 Mar '11

29 Mar '11

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Problem with freesurfer
by Marie ERESUE 29 Mar '11

29 Mar '11

Hi, I'd like to compare registration between FSL and freesurfer. So I have to import my images (I have 25 MRI, 25 CT and 75 SPECT) into freesurfer, with recon-all if I understood. But my images are on NifTi extension and I have error: My program is for 1 image: recon-all -i /home/pmod/Bureau/IRM_ANIMAGE/NORMAUX/image1_IRM.nii -subjid E001 -sd /home/pmod/Bureau/freesurfer/subjects/Marie and I am on Linux 64 bits. How can I do this? Thanks a lot and sorry for this basic question Marie marie_eresue(a)hotmail.fr

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Rhoshel Lenroot is out of the office.
by Rhoshel Lenroot 28 Mar '11

28 Mar '11

I will be out of the office starting 29/03/2011 and will not return until 14/04/2011. I will be checking email intermittently during this time. For urgent matters please contact Julia Hill, julia.hill(a)neura.edu.au, 9399 1268

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Fwd: bbregister bug? with init-spm option--flips left and right
by Tyler Seibert 28 Mar '11

28 Mar '11

Screenshot1 attached ---------- Forwarded message ---------- From: Tyler Seibert <tseibert(a)ucsd.edu> Date: Thu, Mar 17, 2011 at 4:02 PM Subject: bbregister bug? with init-spm option--flips left and right To: freesurfer(a)nmr.mgh.harvard.edu Hello, I hope this is the correct email list--this is my first time posting (just subscribed). I have been using bbregister to calculate a tranformation matrix between a T2 image (T2brain.nii.gz) and the subject's T1.mgz for subsequent use with mri_vol2surf. I have found that the init-fsl option frequently gives very poor registrations (e.g., registered T2 is rotated 30+ degrees from T1). The init-spm option seemed to be working great. However, upon close inspection, I became suspicious this option was actually flipping the T2 so that the left hemisphere became right and vice versa. I am using FreeSurfer version 4.5 and have spm8 referenced in my matlab path. I used a directory ~/bbreg_test in my home directory for the test (linux), which consisted simply of running bbregister with init-fsl and init-spm options. The attached log file (log.txt) contains the commands I used. The terminal output from each test was saved in text files as well, also attached. I have also attached two screenshots of the tkregister2 output for these tests. In each screenshot the far left image is the registered T2 using init-spm, and the far right image is the registered T2 using init-fsl. As the init-fsl version is clearly wrong, the middle image in each screenshot is the init-fsl output again, but manually rotated several degrees to the left to better emphasize the mirror-image relationship between the init-spm (far left) and init-fsl (middle and far right) output images. Please let me know if there is anything further you need from me to investigate this or if there is any insight you can give me as far as how to avoid this error. I noticed at line 209 of the spm_test.txt log file there is a message stating that RAS coordinate system is assumed (see below, where I have copied lines 208-213 for convenience). This may very well be the problem, as the T2brain.nii.gz volume is in LAS, according to mri_info output. However, I do not see where I can override this RAS assumption. >> >> >> >> >> >> >> >> >> /home/tylers/apps/spm8/spm_coreg.m > >> >> >> >> >> INFO: Assuming RAS coordinate system > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using > /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/refvol.spmregister.img > as the target image > >> using > /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/movvol.spmregister.img > as the source image > >> >> >> >> >> >> >> >> >> >> >> >> >> >> > Thank you, -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego

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bbregister bug? with init-spm option--flips left and right
by Tyler Seibert 28 Mar '11

28 Mar '11

Please see the full message below--my first attempt to send failed because I was slightly over the size limit. I will send the images in a subsequent email so you can see the flip for yourself. Tyler ---------- Forwarded message ---------- From: Tyler Seibert <tseibert(a)ucsd.edu> Date: Thu, Mar 17, 2011 at 4:02 PM Subject: bbregister bug? with init-spm option--flips left and right To: freesurfer(a)nmr.mgh.harvard.edu Hello, I hope this is the correct email list--this is my first time posting (just subscribed). I have been using bbregister to calculate a tranformation matrix between a T2 image (T2brain.nii.gz) and the subject's T1.mgz for subsequent use with mri_vol2surf. I have found that the init-fsl option frequently gives very poor registrations (e.g., registered T2 is rotated 30+ degrees from T1). The init-spm option seemed to be working great. However, upon close inspection, I became suspicious this option was actually flipping the T2 so that the left hemisphere became right and vice versa. I am using FreeSurfer version 4.5 and have spm8 referenced in my matlab path. I used a directory ~/bbreg_test in my home directory for the test (linux), which consisted simply of running bbregister with init-fsl and init-spm options. The attached log file (log.txt) contains the commands I used. The terminal output from each test was saved in text files as well, also attached. I have also attached two screenshots of the tkregister2 output for these tests. In each screenshot the far left image is the registered T2 using init-spm, and the far right image is the registered T2 using init-fsl. As the init-fsl version is clearly wrong, the middle image in each screenshot is the init-fsl output again, but manually rotated several degrees to the left to better emphasize the mirror-image relationship between the init-spm (far left) and init-fsl (middle and far right) output images. Please let me know if there is anything further you need from me to investigate this or if there is any insight you can give me as far as how to avoid this error. I noticed at line 209 of the spm_test.txt log file there is a message stating that RAS coordinate system is assumed (see below, where I have copied lines 208-213 for convenience). This may very well be the problem, as the T2brain.nii.gz volume is in LAS, according to mri_info output. However, I do not see where I can override this RAS assumption. >> >> >> >> >> >> >> >> >> /home/tylers/apps/spm8/spm_coreg.m > >> >> >> >> >> INFO: Assuming RAS coordinate system > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using > /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/refvol.spmregister.img > as the target image > >> using > /home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/movvol.spmregister.img > as the source image > >> >> >> >> >> >> >> >> >> >> >> >> >> >> > Thank you, -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego

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Strange issue with isxconcat
by Adam Nitenson 28 Mar '11

28 Mar '11

Hello Freesurfers, I'm having an odd problem with isxconcat. I tried running the command for two separate groups (using Seymour): isxconcat-sess -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/17_FB_Regression_Seed -d /cluster/roffman/users/Stable5_PerRun -analysis SIRP_Stable5 -c Cond1v3 -c Cond1vFix -c Cond3vFix -c Cond1v5 -c Cond1v7 -c Cond5vFix -c Cond7vFix -hemis -o /cluster/roffman/users/Stable5_PerRun/17_FB_Regression_Seed isxconcat-sess -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/17_MTH_Regression_Seed -d /cluster/roffman/users/Stable5_PerRun -analysis SIRP_Stable5 -c Cond1v3 -c Cond1vFix -c Cond3vFix -c Cond1v5 -c Cond1v7 -c Cond5vFix -c Cond7vFix -hemis -o /cluster/roffman/users/Stable5_PerRun/17_MTH_Regression_Seed About an hour in, both commands stop simultaneously and produce the error "MRISread(/cluster/roffman/users/Stable5_PerRun/fsaverage/surf/lh.sphere.reg): could not open file Reading target registration /cluster/roffman/users/Stable5_PerRun/fsaverage/surf/lh.sphere.reg No such file or directory ERROR: could not read /cluster/roffman/users/Stable5_PerRun/fsaverage/surf/lh.sphere.reg" I have since tried re-running the commands, but received the same error, however both groups stopped during different subjects than last time. I'm really not sure what the problem could be, as I have already concanenated these groups for different analyses (including surface analyses, which worked fine). It seems really odd that the commands for both would simultaneously terminate. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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Comparing Sub-cortical Volumes -Mark
by Martin Fletcher 26 Mar '11

26 Mar '11

I am a very new user to Freesurfer and I have a few questions. 1.) Are the sub cortical volumes and thicknesses that Freesurfer generates in the stats output during the recon-all raw volumes (actual volumes) or are they somehow normalized by the time the stats are generated? If they are raw, what sort of transformations must I do to compare them (in order to account for different total head sizes etc.) For instance, if I wanted to compare hippocampal volumes from one subject to another. If they are already normalized is it appropriate to compare subject to subject without any other transformations? 2.) Before using qdec, you must complete a smoothing process for subjects . My understanding is that you have the option of comparing this smoothing to the pre-installed “average subject” or you can do the smoothing process in conjunction with an “average subject” that you create yourself. Is is necessary to create your own “average subject” for each set of studies you do in qdec? Do the cortical thickness comparison change if you are using the already installed “average subject” or if you create your own average subject? Thank you so much. Sincerely, Mark Fletcher eldermarky1(a)yahoo.com

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Freesurfer March 2011