Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

dt_recon error: MatrixReadTxt: could not scan value [1][1]
by Adam Mecca 20 Jan '18

20 Jan '18

Hello FreeSurfer Developers, I'm trying to pre-process some diffusion data based on the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0 I am getting the following warning followed by the program hanging -------------------------- Creating output directory /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon Loading y from /home1/am2359/fs6_data/fpeb_app_fs/fpeb001/dtrecon/dwi-ec.nii.gz ... done reading. MatrixReadTxT: could not scan value [1][1] WARNING: matlab elment type is 1869357167, which is not a matrix. could not allocate 543518770 x 1683973236 matrix Cannot allocate memory unsupported matlab format 1678398324 (unknown) Cannot allocate memory ---------------------------------- I would greatly appreciate your assistance. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: CentOS release 6.9 (Final) 3) uname -a: Linux ariespet.med.yale.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Mar 21 19:29:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) dt_recon.log: see attached Thank you, Adam

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corRead(): can't open file /home/andraderenew/COR-.info
by Renew Andrade 19 Jan '18

19 Jan '18

Hello: I run the command to open freeview -v…(the installation guide example in Bert) and I get the error in I point out in the subject of this email. Thanks for the help in advance! Sincerely, Rene Andrade.

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Hippocampal segmentation flips on the left side
by Tuominen, Lauri Johannes 19 Jan '18

19 Jan '18

Dear Freesurfers, When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to segment an MNI152 template, the resulting segmentation of left hippocampus got flipped in left-right dimension. Otherwise the right hippocampus and other subcortical segmentations in the aseg-file look fine. I encountered a similar problem when I tried to segment a T1 acquired at 7T. I run the command both locally and then on launchpad. Would you know how to fix this? Thanks so much for your advice! Lauri Tuominen

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Incorrect display of control points when image geometries differ
by Antonin Skoch 19 Jan '18

19 Jan '18

Dear experts, I encountered a pitfall with displaying control points in freeView. When the T1 and T2 geometry differs (which can occur for example in hires stream where data are not conformed to 1mm3), it depends on which volume is active when control.dat is loaded. For example, when control.dat is loaded with active T2 (which has different geometry than T1/brainmask), the control points are displayed on the incorrect position of the volume. This affects also loading data on commandline. For example: freeview -v T1.mgz -v T2.mgz -c control.dat displays control points incorrectly. freeview -v T2.mgz -v T1.mgz -c control.dat displays control points correctly. Note, also, that in case of differing geometry of loaded images, the user has to pay special attention to select proper reference volume (brainmask.mgz or other derived images) when control points are created. The choice of reference volume is noted in the official documentation but maybe it can be easily overlooked with serious consequences. To summarize, 4 different cases can occur: control.dat created with reference volume brainmask.mgz, loaded into freeView with active volume brainmask.mgz -> all OK - control points applied correctly and also displayed correctly control.dat created with reference volume brainmask.mgz, loaded into freeView with active volume T2.mgz -> control points applied correctly, but displayed incorrectly (so issue only with display) control.dat created with reference volume T2.mgz loaded into freeView with active volume T2.mgz -> control points applied incorrectly, but displayed correctly in freeView (serious case !!) control.dat created with reference volume T2.mgz displayed with active volume brainmask.mgz -> control points applied incorrectly and also displayed incorrectly Antonin Skoch

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Accounting for WMHs in PETSURFER PVC?
by Elijah Mak 19 Jan '18

19 Jan '18

Hi Doug, Could we tweak the PETSURFER pipeline in order to account for inhomogeneous PET activity in WM due to WMHs? Will running gtmseg with the command --keep-hypo be useful in this context? Thanks for any inputs. Best Wishes, Elijah

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Hippocampal subfield segmentation with T1 and T2
by Cassandra Wannan 19 Jan '18

19 Jan '18

Hi all, I've been trying to run the hippocampal subfield segmentation with T1 and T2 images, and haven't had much luck. I had previously run recon-all on all my scans in v5.3, but testing on one subject I re-ran recon-all with the additional T2 scan, and that seems to have run fine. However, when I try to run the subfield segmentation, I am getting errors. My command line is: recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/T2.mgz CRC040T1T2 -no-isrunning but I have also tried: recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/orig/T2raw.mgz CRC040T1T2 -no-isrunning and: recon-all -s CRC040 -hippocampal-subfields-T1T2 ./CRC040.nii CRC040T1T2 -no-isrunning The error I am getting is: /Applications/freesurfer_v6/bin//mri_robust_register --mov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/norm.mgz --maskmov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//wholeBrainMask.mgz --dst /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/T2.mgz --lta /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta gunzip: can't stat: /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz (/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192) MATLAB:badSwitchExpression Any idea what could be causing the issue? The hippocampal pipeline runs fine without the T2 scan, however I am planning to use the subfield segmentation as a mask for some white matter tractography analysis in FSL, and the dimensions of the output are not close to my nifti files. I was hoping that using the T2 registration would help with this, but can't get it to work! Any help would be greatly appreciated. Kind regards, Cassie

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PET partial volume correction
by John Anderson 18 Jan '18

18 Jan '18

Dear Dr Greeve, I interestingly read the manuscript "Different partial volume correction methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank you for publishing this data. I understood from this paper that he recommended stream for PVC is to correct the PET images using Muller-Gartner method then feed the corrected maps into three group level analyses: surface based for left and right hemispheres then for subcortical regions.. My question is about the subcortical analysis: To describe this analysis, is it a volumetric analysis for subcortical gray matter, or surface based? I am sorry if my questions is basics, I don't have good experience in freesurfer so I want to be sure that I am using the correct terms. Thanks you for any advice! John

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PET partial volume correction
by John Anderson 18 Jan '18

18 Jan '18

3 2

mri_coreg
by John Anderson 18 Jan '18

18 Jan '18

Dear FS developers, Are there any versions of "mri_coreg" that allows to output the registered images. I mean flag "--out or -o" similar to spmregister? Thanks for any guidance John

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motion parameter in preprocessing stream
by Carme Uribe Codesal 18 Jan '18

18 Jan '18

Dear all FreeSurfer users, I was wondering if I can extract any parameter of movement from the recon-all processing using FreeSurfer 5.1. Thanks in advance! Kind regards, Carme

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