[Freesurfer] 전달: fsfast fmcpr was not created.
Hello I did recon-all of dementia patient images. Recon-all -s 0101RG-ana finished without error on the terminal. After I ran fsfast preproce-sess, 7 files didn't exist in the output folder. ;1.register.dof6.dat, 2.fmcpr.nii, 3.fmcor.mc.dat, 4.mcprextreg, 5.fmcpr.sm5.fsaverage.lh.nii, 6.fmcpr.sm5.fsaverage.rh.mii, 7.fmcpr.sm5.mni305.2mm.nii May I redraw and save the recon files using freeview to make fsfast preproce-sess? How can I solve this problem ? Thank you. J. Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] error mni152 reg
Hello Freesurfer mni152reg --s 0201JB-anat => mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': Permission denied. Thus I put this command following the way of searching freesurfer mail support. chmod ugo+w /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253 chmod: cannot access `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': No such file or directory I am using freesurver 5.3 and FDL 5. 0.7. Please let me know what should I do. Thank you. Linux gencess 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux fslregister --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s 0201JB-anat --reg /autofs/cluster/catanagp/users/jumi/subjects/AD/0201JB/0201JB-anat/mri/transforms/reg.mni152.2mm.dat --dof 12 mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': Permission denied ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] Freesurfer/bin/mni152reg version update
Dear Freesurfer team I am a new user in the martinos center. I met a problem when I ran mni152reg on the martinos workstation, gencess. I realized it was a bug related to an old version of mni152reg on the e-mail Freesurfer team sent. Thus I am going to copy a new version of mni152 reg v 2014 into FREESURFER_HOME/bin. But this file only permitted as read only. I know anyone can not be allowed to change the file at FREESURFER_HOME/bin at gencess in the martinos center. To whom may I ask to help change a new version of mni152reg in gencess? Thank you in advance. Best regards, Jung Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] bbresiter tee: disk quota exceeded
Hello freesurfer team When I ran bbregister functional image to T1, I got error message as follows: setenv SUBJECTS_DIR /autofs/cluster/catanagp/users/jumi/subjects/AD/0201JB cd /autofs/cluster/catanagp/users/jumi/subjects/AD/0201JB/0201JB-fsfast/sess01/bold/008/FS /usr/local/freesurfer/stable5_3_0/bin/bbregister --s 0201JB-anat --reg template_to_T1.dat --init-fsl --mov /autofs/cluster/catanagp/users/jumi/subjects/AD/0201JB/0201JB-anat/mri/T1.mgz --o template_to_T1.nii.gz --fslmat template_to_T1.mat --bold -> tee: template_to_T1.dat.log: Disk quota exceeded. $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux gencess 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux tee: template_to_T1.dat.log: Disk quota exceeded. FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_convert /autofs/cluster/catanagp/users/jumi/subjects/AD/0201JB/0201JB-anat/mri/T1.mgz ./tmp.bbregister.15028/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/catanagp/users/jumi/subjects/AD/0201JB/0201JB-anat/mri/T1.mgz... TR=2200.00, TE=1.52, TI=-1.00, flip angle=7.00 i_ras = (-1, 7.45058e-09, 2.23517e-08) j_ras = (8.56817e-08, -1.18744e-08, -1) k_ras = (-2.98023e-08, 1, -2.56114e-09) writing to ./tmp.bbregister.15028/template.nii... tee: template_to_T1.dat.log: Disk quota exceeded. I god this message regarding disk quota exceed to run bbregister for the first time. What is the problem and how can I solve it? Thank you. Best, Jung Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] errors after mri_matrix_multiply and tkregister2
Hello Freesurfer team I got a warning message when I checked tkregister2 after I did mni152.reg, mri_matrix_multiply command. I got warning messages and found that the axial image was suddenly showed up on coronal window view on tkregister2. The error messages as follow like this: [gencess:008] (nmr-stable53-env) tkregister2 --targ $FSL_DIR/data/standard/MNI152_T1_2mm.nii.gz --mov template.nii.gz --reg reg.mni152.dat tkregister_tcl /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl target volume /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz movable volume template.nii.gz INFO: loading target /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. WARNING: pixel size in regfile (2) does not match that of movable volume (3.125) If the movable volume is a bshort or bfloat, make sure that a .bhdr file exists WARNING: slice thickness in regfile (2.00) does not match that of movable volume (3.60) If the movable volume is a bshort or bfloat, make sure that a .bhdr file exists What should I do to get image in a right way? Thank you in advance. Bests, Jung Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] preproc-sess creates files
Hello Freesurfer team When I ran preprc-sess of dementia patient's fmri, fmcpr.nii. files and register.dof6.dat were not created automatically after preproc-sess. Thus I had to bbregister in two dementia patients manually. However recently I did preproc-sess in the another patient, fmcpr.nii and register.dof6.dat were created automatically. Could you please give me any inform what made the difference in creating the results of preproc-sess using the fmri data? Thank you in advance. Bests, Jung Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] tkregister2 erros between bold and mni152 through registeration of T1 to mni152
Hello Freesurfer expert I got two errors when I registered bold image to patient's own T1 image and registered T1 to mni152 and got transform data (reg.mni152. data) between bold and mni152. 1) I typed tkregister2 --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --mov template.nii.gz --reg reg.mni152.dat : target volume /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz movable volume template.nii.gz reg file reg.mni152.dat WARNING: pixel size in regfile (2) does not match that of movable volume (3.125) If the movable volume is a bshort or bfloat, make sure that a .bhdr file exists WARNING: slice thickness in regfile (2.00) does not match that of movable volume (3.60) If the movable volume is a bshort or bfloat, make sure that a .bhdr file exists => What should I do to fix it? 2) I found the result image using tkregister2 was not whole brain covered and part of occipital was cut, when I typed the following commands for resampling functional bold image to mni152 space: mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ --mov template.nii. gz --reg reg.mni152.dat --o template.mni152.nii . If there was not whole brain covered on tkregister2 image view, which step would be failed to create while I registered bold MRI to T1 image and registered T1 image to mni152 and got the transform data created between bold and mni152 ? And how can I fix the result? Best, J. Mi The following commands I wrote and processing results: tkregister2 --mov template.mni152.nii.gz --targ /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz --reg template.mni152.nii.gz.reg tkregister_tcl /usr/local/freesurfer/stable5_3_0/tktools/tkregister2.tcl target volume /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm.nii.gz movable volume template.mni152.nii.gz reg file template.mni152.nii.gz.reg % Screen: 254 252 (40,40,40), inorm = 1, mov_frame = 0 Anat:(127 129 127) ( 1.0 -1.0 -1.0) 5391. 145.1 Func:( 45 54 45) ( 1.0 -1.01.0) 245.428439.9 -- Screen: 274 142 (81,81,81), inorm = 1, mov_frame = 0 Anat:(137 184 127) ( -9.0 -1.0 -56.0) 5701. 153.4 Func:( 50 54 18) ( -9.0 -56.01.0) 478.999580.5 -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] Recon-all terminated abruptly
Hello Freesurfer expert Recon abruptly terminated with error message from the recon-all. log: #@# Skull Stripping Mon Jul 6 13:16:25 EDT 2015 /autofs/cluster/scratch/monday/jungmi/anat_subjects/r0401AG/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) * The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed Killed Linux gencess 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s r0401AG exited with ERRORS at Mon Jul 6 13:16:52 EDT 2015 --- How can I complete recon-all -all ? Thank you in advance. J. Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] unpack error
Hi Freesurfer team I did unpacksdcmdir successfully before at Martinos center. Recently I got error message while I was trying to unpacksdcmdir. ; Cannot open /autofs/cluster/scratch/monday/jungmi/data_parent/0201JB/scan.info There was some messages in unpack.log; INFO: found 4276 Siemens files syngo MR B17 Could not parse NUMARIS version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) WARNING: Run 11 appears to be truncated Files Found: 224, Files Expected (lRep+1): 1 FileName /cluster/archive/309/siemens/TrioTim-35101-20150325-085700-000970/MR.1.3.12.2.1107.5.2.32.35101.2015032509161179360096424 I found the unpack error from two patients data. I don't understand what it happened. How can I use these patients data? Thank you. Jung Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] Recon-all error
Hello Freesurfer expert I got an error message while running recon-all. 1) subject name gencess SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /autofs/cluster/catanagp/users/jumi/subjects/anat/AD0401AG/anat/scripts setenv SUBJECTS_DIR /space/sake/3/users/inverse/subjects cd /autofs/cluster/catanagp/users/jumi/subjects/anat/AD0401AG/anat/scripts 2) the entire command-line executed: in running recon-all CMD mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 3) the error message generated: mri_binarize --i ./tmp.mri_nu_correct.mni.23502/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23502/ones.mgz killed What should I do for re-run recon-all? Thank you. J.Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] recon-all error_cannot find or read transforms/talairach.m3z
Hello Freesurfer expert Running recon-all abruptly stopped with this error message at NMR center; mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 recon-all -s AD0701IB exited with ERRORS 1) subjectname autofs/cluster/catanagp/users/jumi/subjects/anat/AD0701IB 2) Env: source /usr/local/freesurfer/nmr-stable53-env JMi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] mri_convert error
Hello When I tried to run mri_convert brain.mgz to get brain.nii to get betted brain. nii, I received an error message following next: mri_convert -it mgz -i brain.mgz -ot nii -o brain.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from brain.mgz... TR=2530.00, TE=1.64, TI=1200.00, flip angle=7.00 i_ras = (-1, 7.45058e-08, -7.72998e-08) j_ras = (7.35745e-08, 4.30737e-09, -1) k_ras = (1.49012e-08, 1, 1.80444e-09) writing to brain.nii.gz... niiWrite(): error opening file brain.nii.gz ERROR: failure writing brain.nii.gz as volume type 24 What is the problem to convert brain.mgz into brain.nii? How can I fix the error? Thank you. Jung Mi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] FSL GUI error message
Hello When I ran FSL GUI on the Martinos center after typing source freesurfer, I received an error message like that custom widget with id loop-button does not return a valid node on the X-window terminal. How can I solve this problem? Thanks Jung Mi I used FSL 5.0.7, FEAT tool v 6.00 for FSL GUI through the brain vision at Martinos center. Next the information I set: feat main script: /bin/cp /tmp/feat_9l88ef.fsf design.fsf /usr/pubsw/packages/fsl/current/bin/feat_model design mkdir .files;cp /usr/pubsw/packages/fsl/current/doc/fsl.css .files;ln -s /usr/pubsw/packages/fsl/current/doc/images .files/images /usr/pubsw/packages/fsl/current/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/pubsw/packages/fsl/current/bin/feat /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/design.fsf -D /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat -I 1 -init 19094 /usr/pubsw/packages/fsl/current/bin/fsl_sub -T 78 -l logs -N feat2_pre -j 19094 /usr/pubsw/packages/fsl/current/bin/feat /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/design.fsf -D /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat -I 1 -prestats Preprocessing:Stage 1 /usr/pubsw/packages/fsl/current/bin/mainfeatreg -F 6.00 -d /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat -l /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/logs/feat2_pre -R /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/report_unwarp.html -r /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/report_reg.html -i /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/example_func.nii.gz -n 10 -h /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/fsl_T1 -w 3 -x 90 -s /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/5.0.7/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 Option -s ( standard image ) selected with argument "/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/5.0.7/data/standard/MNI152_T1_2mm_brain" ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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.
[Freesurfer] error in FSL group analysis
Hello FS expert
While I ran higher level analysis using FSL feat, I received an error message.
Does it mean this computer needs to update the FSL program?
Computer: brain-vision at martinos center
FS environment 5.3
FSL 5.0.7
/usr/pubsw/packages/fsl/current/bin/fsl_sub -T 60 -l logs -N feat4_post -j 4002
/usr/pubsw/packages/fsl/current/bin/feat
/autofs/cluster/catanagp/users/jumi/jmi_analyses/2ndoutput/.gfeat/cope1.feat/design.fsf
-D
/autofs/cluster/catanagp/users/jumi/jmi_analyses/2ndoutput/.gfeat/cope1.feat
-poststats 1
while executing
"fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -poststats 1" -b 60 -N
feat4_post -h $ID -l logs "
invoked from within
"if { $done_something == 0 } {
if { ! $fmri(inmelodic) } {
if { $fmri(level) == 1 } {
for { set session 1 } { $session <= $fmri(multiple..."
(file "/usr/pubsw/packages/fsl/current/bin/feat" line 389)
1445278890582 addons.update-checker WARN Update manifest for
{972ce4c6-7e08-4474-a285-3208198ce6fd} did not contain an updates property
thank you.
Jung Mi
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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
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