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30132 discussions

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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OASIS-Brains processing with Freesurfer 5
by Gonzalo Rojas Costa 25 Mar '11

25 Mar '11

Hi: I want to re-process some OASIS-BRAINS database images using FS 5. Must I use an recon-all option (because I want that FS use the CP specified) ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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average cortical thickness&intrinsic curvature index
by Liukarl 25 Mar '11

25 Mar '11

Hello, Freesurfer experts: We are extracting the average cortical thickness of each hemisphere for every subject using mris_anatomical_stats. We found that for one subject (attached below), the thickness measures are quite similar but the “intrinsic curvature index” differs drastically between left/right hemispheres. Will this curvature index affect the validity of our thickness measure? Thanks in advance Karl ***the left hemisphere mris_anatomical_stats -l lh.cortex.label -f subject1l.txt subject1 lh limiting computations to label lh.cortex.label. reading volume /usr/local/freesurfer/subjects/subject1/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/subject1/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/subject1/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/subject1/surf/lh.white... structure is "lh.cortex.label" number of vertices = 157421 total surface area = 102165 mm^2 total gray matter volume = 290073 mm^3 average cortical thickness = 2.488 mm +- 0.694 mm average integrated rectified mean curvature = 0.170 average integrated rectified Gaussian curvature = 0.105 folding index = 4980 intrinsic curvature index = 592.3 ***the right hemisphere mris_anatomical_stats -l rh.cortex.label -f subject1r.txt subject1 rh limiting computations to label rh.cortex.label. reading volume /usr/local/freesurfer/subjects/subject1/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/subject1/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/subject1/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/subject1/surf/rh.white... structure is "rh.cortex.label" number of vertices = 158401 total surface area = 102285 mm^2 total gray matter volume = 291519 mm^3 average cortical thickness = 2.482 mm +- 0.707 mm average integrated rectified mean curvature = 0.173 average integrated rectified Gaussian curvature = 0.299 folding index = 5756

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problem of correction for multiple comparisons in sarfece based analyses
by Habets P (SP) 25 Mar '11

25 Mar '11

Dear Freesurfer users, Which is to most preferably correction for multiple comparisons when investigating surface based cortical thickness changes between groups in smoothed data. Furthermore subjects between groups are related in other words not independent from each other. It is not clear for me whether FDR or cluster wise correction is feasible in highly smoothed and data that does not fulfill the criteria of independence. Best wishes, Petra Habets [cid:image001.jpg@01CBEAD1.5ACD2790] Petra Habets PhD-Student School for Mental Health and Neuroscience p.habets(a)maastrichtuniversity.nl <mailto:p.habets@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl> Vijverdalseweg 1, 6226 NB Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T + 31 43 368 8659 F + 31 43 368 8689 Note: the email addresses have changed! [cid:image002.jpg@01CBEAD1.5ACD2790]Please consider your environmental responsibility before printing this e-mail.

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The atlas specification
by Youngsang Cho 25 Mar '11

25 Mar '11

Hi, everybody. I am wondering the specification of the atlas which is used for surface registration. Please answer what kinds of subjects are used and how many subjects are used to generate the atlas included in Freesurfer. Or please tell me the link about the atlas specification. Sincerely, Youngsang Cho

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Vertex-by-vertex analyses within ROIS?
by Dalwani, Manish 24 Mar '11

24 Mar '11

Hello Freesurfers, We are interested in comparing cortical thickness in 2 groups. Due to small sample size (and thus less power), we are swaying away from whole-brain vertex analyses. Instead we would like to compare specific ROIs between two groups. We understand that we can get an estimate of average cortical thickness from each ROI. We fear that by comparing those estimates over a large ROI may cause it to be less sensitive in picking up a very small region of severe cortical thinning. Therefore, our questions are as follows: 1. Can we perform vertex-by-vertex analyses between groups but not on whole-brain and only on the specific apriori ROIs? 2. If we can do vertex-by-vertex ROI analyses, is there a reasonable statistical method to correct for multiple comparisons? Kindly advise! Regards, Manish Dalwani Sr. PRA Dept. of Psychiatry University of Colorado Denver Tel: 303-724-3185 Email: manish.dalwani(a)ucdenver.edu

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N3 correction issues
by Nandita Vijayakumar 24 Mar '11

24 Mar '11

Hi all, We are processing longitudinal structural MRI data on Freesurfer 5. 0. As our images have some intensity problems, we were running an N3 correction outside of FreeSurfer using a mask in order to maximize this step (as per recommended by Boyes et al., 2008). We first ran autorecon1 and then used the brainsmask.mgz as a mask for the N3 correction, using the following steps. mri_convert orig.mgz orig.mnc mri_binarize --i brainmask.mgz --min 1 --o binmask.mgz* mri_convert binmask.mgz binmask.mnc* mincnorm orig.mnc orig_norm.mnc nu_correct -mask binmask.mnc -distance 50 -iterations 1000 -stop 0.0001 -shrink 2 -fwhm .05 orig_norm.mnc nu.mnc mri_convert nu.mnc nu.mgz* This nu.mgz was then fed into freesurfer and autorecon1 was run over again without nuintensity correction. However, during this step, many of our scans are crashing, with the T1.mgz being very dark. When the same scans were run through Freesurfer with the nuintensitycor-3T flag (without using a mask), there were no crashes. Do you have any advice on why the N3 correction using the mask is crashing when re-running autorecon 1? Should we be using different nu_correct parameters to help the process? Thanks for your help! Nandi

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Fwd: fMRI and anatomical T1 overlaid
by leonardo kay 24 Mar '11

24 Mar '11

Thanks Doug. After doing reg-feat2anat , I checked the registration and overlaid zstat file: tksurfer subjectid rh inflated -overlay featdir/rendered_thresh_zstat1.nii.gz I have attached an image of tksurfer interface . I'm not quite sure about what blue and red clusters mean. They are suposed to be activations, but I'm not watching the same in FSL-view. Could you give me a hand please? Am I using the right stat file? Thanks in advance best regards. ---------- Forwarded message ---------- From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Date: 2011/3/23 Subject: Re: [Freesurfer] [Fressurfer] fMRI and anatomical T1 To: leonardo kay <leonardo.kay(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu There is a tutorial on this on our wiki. Basically, you need to run reg-feat2anat to get a registration file, then run tksurfer passing it the registration file and the stat volume as the overlay. doug leonardo kay wrote: > Hi all > > Can anyone help me overlaying fMRI activations from fsl on a anatomical T1 > volume in freesurfer. > Is there any previous format conversion to do before? > > Thanks in advance > best regards, > > -- > Leo Kay. > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Leo Kay.

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