Freesurfer

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30084 discussions

recon-all reconstruction problems
by salvatoreandrea.92＠libero.it 08 Dec '15

08 Dec '15

Hi Freesurfer experts! I had run recon-all over 5 T1s acquired in different time-points in a patient affected by Multiple Sclerosis. Looking at the surfaces created by recon-all it appears that almost all the frontal lobe is missing, probably due to the big demyelinating lesion that she has. However this lesion does not affect the gray matter, which is still there, as I could see by the T1 images. Can I do something to correct for this error? Also because these distortions may have contaminated the stats files that, if I am not wrong, contain the volumes of several areas in the brain. Attached you can find a snapshot of the left hemisphere of the patient. Thank you all, Salvatore

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Recon-all -bigventricles option : general use or not in Alzheimer cases ?
by Matthieu Vanhoutte 08 Dec '15

08 Dec '15

Dear FreeSurfer experts, My question is in the title. I'm working on Alzheimer case where most of the cases have large ventricles. Is it better in general use to apply -bigventricles option on all subjects (for homogeneous calculus or something like that...) or to distinct subtle cases of patients with not so big ventricles ? Thanks in advance for helping ! Best regards, Matthie

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Re: [Freesurfer] Freesurfer 6 - exited with errors
by Scott Quadrelli 08 Dec '15

08 Dec '15

Thanks Doug and Bruce for your response. Here is the result of the command Doug requested: $ mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab C02DL_t1 rh white INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/mri/wm.mgz... reading input surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white... Using TH3 vertex volume calc Total face volume 229272 Total vertex volume 224839 (mask=0) reading input pial surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.pial... reading input white surface /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white... reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/6.0.beta/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1539395 mm^3 (det: 1.265500 ) lhCtxGM: 216981.653 216526.000 diff= 455.7 pctdiff= 0.210 rhCtxGM: 224488.981 223971.000 diff= 518.0 pctdiff= 0.231 lhCtxWM: 221893.625 222489.000 diff= -595.4 pctdiff=-0.268 rhCtxWM: 224605.205 224852.000 diff= -246.8 pctdiff=-0.110 SubCortGMVol 51078.000 SupraTentVol 967354.464 (965462.000) diff=1892.464 pctdiff=0.196 SupraTentVolNotVent 940904.464 (939012.000) diff=1892.464 pctdiff=0.201 BrainSegVol 1111453.000 (1108301.000) diff=3152.000 pctdiff=0.284 BrainSegVolNotVent 1080460.000 (1080411.464) diff=48.536 pctdiff=0.004 BrainSegVolNotVent 1080460.000 CerebellumVol 141268.000 VentChorVol 26450.000 3rd4th5thCSF 4543.000 CSFVol 1413.000, OptChiasmVol 158.000 MaskVol 1614399.000 663 321 1164 2.414 0.317 0.126 0.029 10 0.7 BA1_exvivo 1878 1200 2522 2.055 0.423 0.096 0.018 13 1.5 BA2_exvivo 846 653 728 1.608 0.324 0.159 0.035 9 1.3 BA3a_exvivo 1782 1155 1902 1.588 0.371 0.089 0.018 9 1.5 BA3b_exvivo 930 539 1396 2.423 0.439 0.108 0.030 8 1.4 BA4a_exvivo 1048 718 1669 2.480 0.403 0.093 0.021 4 1.0 BA4p_exvivo 6264 3392 9732 2.494 0.482 0.103 0.030 66 7.5 BA6_exvivo 951 631 1818 2.403 0.428 0.123 0.027 16 1.1 BA44_exvivo 915 650 1780 2.212 0.349 0.139 0.031 16 1.0 BA45_exvivo 3074 2189 3724 1.675 0.473 0.134 0.035 33 4.8 V1_exvivo 4690 2886 4907 1.698 0.528 0.151 0.041 79 8.3 V2_exvivo 324 198 535 2.216 0.477 0.135 0.036 5 0.5 MT_exvivo 285 170 847 3.400 0.783 0.132 0.036 4 0.4 perirhinal_exvivo 245 177 522 2.386 0.732 0.126 0.020 2 0.2 entorhinal_exvivo The annotation seems to be fine, I have attached a screenshot of the second command. The initial command I ran was: "recon-all -all -s bert -hippocampal-subfields-T1” However I noticed there was no [lr]h.hippoSfLabels-T1.v10.mgz output. When I tried to run the just the hippocampal segmentation I got an error that the matlab dependencies weren’t installed, so presumably that is why I received the original message ?! Cheers, Scott From: "quadrellis(a)me.com" <quadrellis(a)me.com> Date: Tuesday, 8 December 2015 8:57 am To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer 6 - exited with errors Hi All, I am trying to track down the source of an error on one of my first runs using freesurfer 6. I have attached the relevant logs. Any help would be much appreciated. Cheers, Scott

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Freesurfer 6 - exited with errors
by Scott Quadrelli 07 Dec '15

07 Dec '15

Hi All, I am trying to track down the source of an error on one of my first runs using freesurfer 6. I have attached the relevant logs. Any help would be much appreciated. Cheers, Scott

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Freesurfer V6 (beta) and MacOS 10.11 (El Capitan)
by Kevin Aquino 07 Dec '15

07 Dec '15

Dear all, I was wondering if many users have had freesurfer 6 (beta) working (well) with Mac OS 10.11? (or Freesurfer V5.3) Thanks! *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* www.physics.usyd.edu.au/~aquino/ ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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Left and right white matter intensity ratio
by Sabrina Yu 07 Dec '15

07 Dec '15

Hi there, Would it be possible to use pctsurfcon to calculate the ratio of white matter signal intensity between left and right hemispheres? Thank you Sabrina

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FDR in FS-FAST
by stdp82＠virgilio.it 07 Dec '15

07 Dec '15

Hi list,I have two concerns, please:1) It is possible to apply FDR correction on rs-fMRI seed based analysis by FS-FAST? If yes, I can I do it?2) I have apply the FS guidelines and I have used Montecarlo correction with threshold at 1.3 but in the within group analysis the clusters are very large. In the guide I read examples with a threshold at 3. Is there a specific reason?Thanks Stefano

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Recon-all Bug: Applying Pial Edits with -FLAIRpial Option
by Tori Williams 07 Dec '15

07 Dec '15

Hello, I am running Freesurfer version 5.3.0 with the FLAIR surface refinement bbregister patch installed. I have recently encountered a problem with applying pial edits concurrently with the option of surface adjustment using T2 FLAIR scans during recon-all. After initially running recon-all with the FLAIR option flags: 'recon-all -subjid <subj> -all -FLAIR <flair_scan.mgz> -FLAIRpial' I had tried to apply pial edits without the -FLAIRpial flag on the 2nd recon assuming the adjustments would carry over.: 'recon-all -subjid <subj> -autorecon-pial' This did not work out and the surfaces were worse than before as T2 adjustments were not applied. I then reran the same command adding the -FLAIRpial option: 'recon-all -subjid <subj> -autorecon-pial -FLAIRpial' Although the surfaces were better due to the T2 adjustment and similar to the initial recon, recon-all did not apply any of the pial edits. This was odd because other scans that required control points (with '-autorecon2-cp -autorecon3') or white matter edits (with 'autorecon2-wm -autorecon3') did apply all manual edits, including adjusting the pial surfaces for deleted voxels and refining by the T2 scans. After some detective work looking into the log file and recon-all code, I think I may have found the problem. Turns out, just in the case of pial edits, the ?h.woFLAIR.pial files are not being re-written to reflect the new surfaces correcting for edited voxels following the "Make Pial Surf" step. This is noted in the date stamp of the ?h.woFLAIR.pial files being older than all other surface files following the last recon-all procedure. This is likely because the ?h.pial output files from the "Make Pial Surf" are being overwritten by the "Refine Pial Surfs w/ T2/FLAIR" procedure, instead of being copied over to the ?h.woFLAIR.pial files which are the input to the FLAIR adjustment, and would thus carry on the pial edits. Here is the recon-all code: set nv1=(`mris_info $sdir/${hemi}.pial |& grep nvertices`) set nv2=(`mris_info $sdir/${hemi}.wo${t2flair}.pial |& grep nvertices`) if ( (! -e $sdir/${hemi}.wo${t2flair}.pial) || \ ("$nv1" != "$nv2") ) then set cmd = (cp -v $sdir/${hemi}.pial $sdir/${hemi}.wo${t2flair}.pial) I have attached the log file for one of my subjids that had this issue (Note, the 10/20/15 recon-all is after installing the patch due to the bbregister issues, and the last recon-all on 12/2/15 I tried starting the stream earlier with the -autorecon2-wm flag just to see if that would help). I think it would help to just copy the ?h.pial to ?h.woFLAIR.pial regardless of nvertices being the same. Please let me know if I can provide any more information! Thank you for your time and support! Victoria J. Williams, PhD Postdoctoral Fellow VA Boston Healthcare System Jamaica Plain Neuroimaging Research for Veterans Center (NeRVe) Memory Disorders Research Center 150 South Huntington Ave D11-102 Boston, MA 02130

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Error with mri_nu_correct.mni in recon-all
by 木村一皓 07 Dec '15

07 Dec '15

Hi, I've recently used freesurfer after installing MINC Tool Kit, and got some problem. Seeing the log file, the problem seems to be in mri_nu_correct.mni with the following command. mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz I've attached the log file and error.log when I've done this separately. Before installing MINC Toolkit, I've done the process without problem for sure, so I think MINC-toolkit caused some error.. I found some threads about the error in mri_nu_correct.mni, but I couldn't find the answer. Does somebody has any solution or suggestion for this? Best, Ikko

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including missing gray matter voxels
by Kendrick Kay 04 Dec '15

04 Dec '15

I am trying to figure out how to manually expand the pial surface boundary (generated via automatic segmentation with recon-all) to include additional gray matter voxels which have been erroneously labeled as skull or CBF. i found extensive documentation on how to delete voxels (for example from white matter mask), but i can't seem to find relevant information advising how to manually include some missing gray matter voxels (on either ends of the cortex - i.e. white matter/gray matter boundary or gray matter/pial surface boundary). Any help would be appreciated. -- Kendrick Kay, PhD Assistant Professor Center for Magnetic Resonance Research University of Minnesota, Twin Cities Web: http://cvnlab.net <http://cvnlab.net/> E-mail: kay(a)umn.edu <mailto:kay@umn.edu> Cell: 510-206-1059 Skype: kendrickkay

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