Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Linear Mixed Effect Modle
by lanbo Wang 22 Jan '18

22 Jan '18

Hi, all experts. When I try to use LME model. There is a code "mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh" in LME tutorials website under *"b)Mass-univariate". * When I ran it, error happened: """ [mtobia@localhost PD]$ mris_preproc --qdec-long $SUBJECTS_DIR/sub_long.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.long.mgh nsubjects = 80 ERROR: cannot find /HD4/PD/Patients_Symptom//.long. """ And I already check the file name, The folder name match <fsid>.long.<fsid_base>. What should I do now? Thanks for your help. Best, Lanbo

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TRACULA QC
by Linnea Marie Dramdal Borg 22 Jan '18

22 Jan '18

Hi, We have run into some issues with our tractographies. I have attached examples: In "fmajor_4053.png", there is a "bridge" in forceps minor on its way to the frontal lobe. We've also come across other cases of bridging in forceps minor, such as "fminor_4013". Also, there are some voxel paths that are rather weak, such as "unc_2068_1.png" and "unc_3022_1.png"/"unc_3022_2.png". This does not seem optimal. Do you agree? We've also come across a couple of cases where it hasn't really found the tract correctly, such as in "29_ccg_1", "unc_3045_1.png" and "268_ccg.png". This also includes "fmm_32.png", which has a nice voxel intensity, but neither the forceps minor nor major voxels really fit their underlying tracts. Finally, neither "unc_3068_2.png" nor "unc_4040.png" are really correct. Should we reinitialize all of them, or can we use some of them without affecting the results too much? Thank you, Linnea Marie

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convert nii to nii.gz
by Ting Li 22 Jan '18

22 Jan '18

Hi Freesurfer Expert, I am very new to Freesurfer and have a very basic question. How to convert .nii files to nii.gz? I have tried the mri_convert subject_name.nii to subject_name.nii.gz directly. It gives me an error information that mri_convert: command not found. Thanks for your help! Best, Ting

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bert log file
by Renew Andrade 21 Jan '18

21 Jan '18

Hello everyone!I write to you because I can't get the process done in freesurfer. I attach the log file. Thank you!

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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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Freesurfer January 2018