Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

FW: poor grey/white distinction in superior part of scan
by Matt Glasser 24 Jan '14

24 Jan '14

From: Christine Smith <cnsmith(a)ucsd.edu> Date: Thursday, January 23, 2014 3:58 PM To: Matt Glasser <matt(a)ma-tea.com> Subject: Re: [Freesurfer] poor grey/white distinction in superior part of scan Please note that the left and right sides of the brain are flipped for freesurfer vs the dicom picture. Please find attached a dicom picture that is oriented the same way as freesurfer. Sorry for any confusion. On Thu, Jan 23, 2014 at 1:56 PM, Christine Smith <cnsmith(a)ucsd.edu> wrote: > Dear Matt, > > Please find attached two pictures. One is of the brain from reconstructed > dicom files (using AFNI). The other one is a pic from tkmedit of the same > subject and approximately the same slice of brain. Notice that the freesurfer > image is very bright. Look at the white matter and pial lines (i.e., cortical > thickness) in the upper left hand part of the image and see how thin the > cortex appears. Notice also, that there is very little grey/white contrast in > this same area in the brain image reconstructed from dicoms. > > Please let me know if there are any other pictures you might desire or > information you might need. > > Christine > > > On Thu, Jan 23, 2014 at 11:33 AM, Matt Glasser <matt(a)ma-tea.com> wrote: >> Some pictures would probably be helpful to know what the issue is. >> >> Peace, >> >> Matt. >> >> From: Christine Smith <cnsmith(a)ucsd.edu> >> Date: Thursday, January 23, 2014 1:05 PM >> To: <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: [Freesurfer] poor grey/white distinction in superior part of scan >> >> Hello, >> >> I am emailing to inquire about whether poor grey/white contrast in one part >> of a scan (i.e., the posterior and superior part of the scan; ~parietal >> cortex) can be addressed. The contrast in other parts of the scan looks good >> and freesurfer does a great job of distinguishing white from grey. For the >> parietal cortex area the cortex appears very thin. In addition, the entire >> brain appears 'white' or bright, even though the brain doesn't look this >> bright if you reconstruct it from dicoms. >> >> We have now obtained 4 scans like this, so it isn't just one person with >> thinning cortex. >> >> How can I make an adjustment to only this superior part of the brain and >> leave the rest of it alone? Or do I need to make an adjustment to the >> intensity early on for the entire scan and then basically start over with >> editing? >> >> Best, >> Christine >> >> -- >> Christine N. Smith, Ph.D. >> Department of Psychiatry >> University of California, San Diego >> _______________________________________________ Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listin >> fo/freesurfer 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. > > > > -- > Christine N. Smith, Ph.D. > Department of Psychiatry > University of California, San Diego -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

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Fwd: QDEC error
by Wanda Truong 23 Jan '14

23 Jan '14

---------- Forwarded message ---------- From: Wanda Truong <wanda.truong.87(a)gmail.com> Date: 23 January 2014 16:57 Subject: QDEC error To: freesurfer(a)nmr.mgh.harvard.edu Hello, I am having trouble with my group analysis using QDEC. I have 3 groups, 72 subjects, and 4 covariates. This is the error I get: Loading data table /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/qdec.table.dat... Number of columns: 438 fsid column: 1 Number of factors: 437 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I've attached my qdec.table.dat file and fsgd file as well. I initially created the columns using excel and I copied and pasted it into a .txt. file. Could this be the problem? If so, what would be a better method? Thanks very much, Wanda -- Wanda Truong, MSc -- Wanda Truong, MSc

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Corrections to the segmentation lead to giant defects
by Thomas Fink 23 Jan '14

23 Jan '14

Dear Freesurfer experts, We are using FS 5.1 and have several participants with errors in the segmentation of the hippocampus and other regions of the cortex. So far we did corrections to the hippocampus but in 10 out of 13 participants we got error messages listed below: Seven participants: ----- CORRECTING DEFECT 0 (vertices=74686, convex hull=1605) Excessive topologic defect encountered: could not allocate 390335770 edges for retessellation Cannot allocate memory Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 ----- One participant: ----- mhtVoxelList_Add(189, 240, 290, 260205): complete list too big! mhtVoxelList_Add(189, 240, 290, 260205): complete list too big! No such file or directory marking ambiguous vertices... Too many intersected faces for face 255461 (126442, 128896, 128873) No such file or directory Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 ----- One participant: ----- CORRECTING DEFECT 14 (vertices=33317, convex hull=1285) mris_fix_topology(26738) malloc: *** mmap(size=1212047360) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 ----- One participant: ----- Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 414500 ambiguous faces found in tessellation segmenting defects... Bus error Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 ----- The error log says in all cases that there is something wrong with the cerebellum. When we open the ?h inflated.nofix file then we see the cerebellum added (see attached file) in the hemisphere we made the edits. We have no clue if or what we are doing wrong and here are the steps we did: - open the files (tkmedit subject norm.mgz -aseg.mgz - Tool -> Configure Segmentation Brush info -> select the hippocampus -> add voxels - File -> save segmentation - run recon with "recon-all -autorecon2 -noaseg –autorecon3 -subjid subject -nuintensitycor-3T" So far we had no problems with our subjects for all the previous steps (recon after wm, pial, .... edits) and it did run smoothly. Any help would be greatly appreciated. Thomas Fink Mail: Thomas.Fink(a)psy.lmu.de

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Help Thickness Reproducibility
by Thiago Junqueira 23 Jan '14

23 Jan '14

Dear FreeSurfers I am having some troubles to run step 4 of protocol to thickness reproducibility. The error message is below: nf04:~> mris_surface_stats -nsmooth 100 -surf_name /home/nf04/subjects/t_pac01/su > > rf/lh.white -out_name > > /home/nf04/subjects/groupstudy/lh_std_60.mgh -absmean > /home/nf04/subjects/groupstudy/lh_absmean_60.mgh -mean > /home/nf04/subjects/groupstudy/lh_mean_60.mgh -absstd > /home/nf04/subjects/groupstudy/lh_absstd_60.mgh > > /home/nf04/subjects/groupstudy/tpac02_lh_thicknes_diff_resampled_to_tpac01.mgh > Perform 100 steps of smoothing of input data > using /home/nf04/subjects/groupstudy/lh_std_60.mgh as output file > using /home/nf04/subjects/groupstudy/lh_absmean_60.mgh as output file > for > abs-mean > using /home/nf04/subjects/groupstudy/lh_mean_60.mgh as output file for > mean > using /home/nf04/subjects/groupstudy/lh_absstd_60.mgh as output file > for > std-of-abs-mean > reading > > /home/nf04/subjects/groupstudy/tpac02_lh_thicknes_diff_resampled_to_tpac01.mgh... > Smooth input data by 100 steps > ERROR: MyMRISsmooth: Surf/Src dimension mismatch > Stats over surface (76117 vertices): mean = 0.368766, std = 1.02826, > absmean = 0.790395, absstd = 0.754038 > > I would appreciate so much any help. > > Many thanks > Thiago Junqueira Medical Physicist, Msc Student in Neuroimage Neuroimage Lab and Medical Physics Lab University of Campinas Phone: +55 19 8809-9476

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mri_surfcluster
by krista kelly 23 Jan '14

23 Jan '14

Hi all, I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work: mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh the error = srcsubjid must be supplied If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong? Thanks! Krista

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poor grey/white distinction in superior part of scan
by Christine Smith 23 Jan '14

23 Jan '14

Hello, I am emailing to inquire about whether poor grey/white contrast in one part of a scan (i.e., the posterior and superior part of the scan; ~parietal cortex) can be addressed. The contrast in other parts of the scan looks good and freesurfer does a great job of distinguishing white from grey. For the parietal cortex area the cortex appears very thin. In addition, the entire brain appears 'white' or bright, even though the brain doesn't look this bright if you reconstruct it from dicoms. We have now obtained 4 scans like this, so it isn't just one person with thinning cortex. How can I make an adjustment to only this superior part of the brain and leave the rest of it alone? Or do I need to make an adjustment to the intensity early on for the entire scan and then basically start over with editing? Best, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

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Time taken by Freesurfer for processing
by Tanya Verma 23 Jan '14

23 Jan '14

Hi, I would like to ask that why does the Freesurfer takes so much time for processing particularly autorecon2 ? Knowing that Freesurfer takes a lot of time for processing, why is it still used widely by researchers ? For segmentation followed by volume calculation , does one has to really wait for hours for the results? Thank you

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Hippocampal volume estimation
by Tanya Verma 23 Jan '14

23 Jan '14

Hello, I have to segment out hippocampus only and calculate its volume. Since FreeSurfer segments out many sub-cortical structures and their respective volumes, it takes a lot of time ( more than 10 hours ). Is there any way to extract a particular sub-cortical structure only from brain ( hippocampus in my case ) without taking a lot of time? Thank you

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Problems converting MNC to NII
by Caspar M. Schwiedrzik 23 Jan '14

23 Jan '14

Hi! I am having some troubles converting MNC files to NII while preserving the exact values in the MNC file. I have tried to use mri_convert and mnc2nii, but in both cases, the values in the file output get changed. The help of mri_convert mentions that the output for MNC files may not work. Is there a workaround or a recommended procedure to convert MNC into NII? Thanks, Caspar

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glm specification in longitudinal analyses for one group
by Sandra Preissler 22 Jan '14

22 Jan '14

Dear freesurfer experts and users At the moment our group is working on longitudinal analyses for two different time points in one group. Our analyses worked well and we tried to calculate the effects of six different covariates and one fix moderator variable (we had two different MRI Scanner and tried to consider this effect) with the function mri_glmfit. We did pre-processing with mri_preproc: mris_preproc --fsgd extra_komplett.fsgd --cache-in long.thickness-rate.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.extra_komplett.thickness.10.mgh With the fsgd-File designed like the following example: GroupDescriptorFile 1 Title G1V2 Class Scannertyp-Main Variables z1 z2 z3 z4 z5 z6 Input P01 Scannertyp-Main T3 z11 z21 z31 z41 z51 z61 Because of the consideration of the variable Scanner we designed the design matrix on our own. Before calculating the effect of the covariates we calculated the main effect (for the assumed underlying regression model please refer to equation number 1 in the attached pdf). For doing this we built a contrast file (please refer to equation 2). In a longer discussion we decided to delete different covariates and get the regression model shown in equation 3 (and the contrast file for the main effect in equation 4). Surprisingly both main effects not even were similar. Therefore we tried two different models (please refer to equation 5 and 7 for the two regression models). If the underlying model is a normal linear model the first three Contrasts and regression models should gave the same results. In our analyses we have really different results, therefore we have problems in interpreting and understanding the underlying general linear model. There seems to be still an influence of the covariates even if there are modeled with 0 (which in our understanding means they were mathematically not included in the model). Is the probability dependent on the distribution of the covariates even if they are modeled with no influence? If so, how is the belonging regression model? The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64 Can you help us in fixing this theoretical problem? Thanks in advance! Sandra ---------------------------------------------------------------- This message was sent through https://webmail.uni-jena.de

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Freesurfer January 2014