[Freesurfer] Brainstem segmentations (6.0)
Hello Experts, We used the brainstem segmentation that is built into FS 6.0, to interrogate midbrain volumes. My question was: the way FS segments the midbrain, does it include the cerebral peduncles? cheers,Cat___ 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] freeview read error
Dear Experts, I am trying to use Freeview to view volumes using the command listed on the website: http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the only volume that loads is the aseg. I am not able to load the T1, wm, or brainmask mgz’s . either from the terminal or through the FreeView gui. I am using Freesurfer 5.3 and have downloaded XQuarz on a Mac OSX Lion 10.7.5 workstation.Below is the command I am using and the terminal output. I would very much appreciate any help or insight.cheers,cat Below is my command: freeview -v \C1023_out/mri/T1.mgz \C1023_out/mri/wm.mgz \C1023_out/mri/brainmask.mgz \C1023_out/mri/aseg.mgz:colormap=lut:opacity=0.2 \-f C1023_out/surf/lh.white:edgecolor=blue \C1023_out/surf/lh.pial:edgecolor=red \C1023_out/surf/rh.white:edgecolor=blue \C1023_out/surf/rh.pial:edgecolor=red Terminal error: Freeview[4393:703] invalid drawableFreeview[4393:703] invalid drawableFreeview[4393:703] invalid drawableFreeview[4393:703] invalid drawableFreeview[4393:703] invalid drawableFreeview[4393:703] invalid drawableFreeview[4393:703] invalid drawableFreeview[4393:703] invalid drawablemghRead(/Volumes/home/Documents/xx/C1023_out/mri/T1.mgz, -1): read errormghRead(/Volumes/home/Documents/xx /C1023_out/mri/T1.mgz, -1): read errorMRIread failed: Unable to read from /Volumes/home/Documents/xx /C1023_out/mri/T1.mgzmghRead(/Volumes/home/Documents/xx /C1023_out/mri/wm.mgz, -1): read errorMRIread failed: Unable to read from /Volumes/home/Documents/xx /C1023_out/mri/wm.mgzmghRead(/Volumes/home/Documents/xx /C1023_out/mri/wm.mgz, -1): read errormghRead(/Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgz, -1): read error MRIread failed: Unable to read from /Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgzmghRead(/Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgz, -1): read error ___ 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.
Re: [Freesurfer] freeview read error
Hi Bruce, Yes, they exist.but this seems strange...-rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 T1.mgz -rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 wm.mgz -rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 brainmask.mgz On Wednesday, August 26, 2015 12:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Cat do those file exist? What does ls -l tell you for them? Bruce On Wed, 26 Aug 2015, Cat Chong wrote: Dear Experts, I am trying to use Freeview to view volumes using the command listed on the website: http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the only volume that loads is the aseg. I am not able to load the T1, wm, or brainmask mgz’s . either from the terminal or through the FreeView gui. I am using Freesurfer 5.3 and have downloaded XQuarz on a Mac OSX Lion 10.7.5 workstation. Below is the command I am using and the terminal output. I would very much appreciate any help or insight. cheers, cat Below is my command: freeview -v \ C1023_out/mri/T1.mgz \ C1023_out/mri/wm.mgz \ C1023_out/mri/brainmask.mgz \ C1023_out/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f C1023_out/surf/lh.white:edgecolor=blue \ C1023_out/surf/lh.pial:edgecolor=red \ C1023_out/surf/rh.white:edgecolor=blue \ C1023_out/surf/rh.pial:edgecolor=red Terminal error: Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable mghRead(/Volumes/home/Documents/xx/C1023_out/mri/T1.mgz, -1): read error mghRead(/Volumes/home/Documents/xx /C1023_out/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /Volumes/home/Documents/xx /C1023_out/mri/T1.mgz mghRead(/Volumes/home/Documents/xx /C1023_out/mri/wm.mgz, -1): read error MRIread failed: Unable to read from /Volumes/home/Documents/xx /C1023_out/mri/wm.mgz mghRead(/Volumes/home/Documents/xx /C1023_out/mri/wm.mgz, -1): read error mghRead(/Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgz, -1): read error MRIread failed: Unable to read from /Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgz mghRead(/Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgz, -1): read error ___ 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 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.
Re: [Freesurfer] freeview read error
no, seems to be plenty left.. 240 TB On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: they are empty (zero size). Maybe your disk filled up? On Wed, 26 Aug 2015, Cat Chong wrote: Hi Bruce, Yes, they exist. but this seems strange... -rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 T1.mgz -rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 wm.mgz -rwx--+ 1 mxx MF\Domain Users 0 Aug 26 09:12 brainmask.mgz On Wednesday, August 26, 2015 12:04 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Cat do those file exist? What does ls -l tell you for them? Bruce On Wed, 26 Aug 2015, Cat Chong wrote: Dear Experts, I am trying to use Freeview to view volumes using the command listed on the website: http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the only volume that loads is the aseg. I am not able to load the T1, wm, or brainmask mgz’s . either from the terminal or through the FreeView gui. I am using Freesurfer 5.3 and have downloaded XQuarz on a Mac OSX Lion 10.7.5 workstation. Below is the command I am using and the terminal output. I would very much appreciate any help or insight. cheers, cat Below is my command: freeview -v \ C1023_out/mri/T1.mgz \ C1023_out/mri/wm.mgz \ C1023_out/mri/brainmask.mgz \ C1023_out/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f C1023_out/surf/lh.white:edgecolor=blue \ C1023_out/surf/lh.pial:edgecolor=red \ C1023_out/surf/rh.white:edgecolor=blue \ C1023_out/surf/rh.pial:edgecolor=red Terminal error: Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable Freeview[4393:703] invalid drawable mghRead(/Volumes/home/Documents/xx/C1023_out/mri/T1.mgz, -1): read error mghRead(/Volumes/home/Documents/xx /C1023_out/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /Volumes/home/Documents/xx /C1023_out/mri/T1.mgz mghRead(/Volumes/home/Documents/xx /C1023_out/mri/wm.mgz, -1): read error MRIread failed: Unable to read from /Volumes/home/Documents/xx /C1023_out/mri/wm.mgz mghRead(/Volumes/home/Documents/xx /C1023_out/mri/wm.mgz, -1): read error mghRead(/Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgz, -1): read error MRIread failed: Unable to read from /Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgz mghRead(/Volumes/home/Documents/xx/C1023_out/mri/brainmask.mgz, -1): read error ___ 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 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 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] TRACULA- DKI?
Dear Tracula Team, Quick question: Is Tracula able to to process diffusion kurtosis data, and yield, let's say, 'mean kurtosis' parameters for specific fiber tracts?cheers,Cat___ 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] tracula min mid max values
Dear Anastasia, I am trying to visualize the tract p-values along one pathway as shown in the tutorial.http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics I have implemented the p-values into a text file but I am uncertain of what the settings for the heat scale thresholds ought to be , i.e. I am unsure of what to set the min, mid, max and offset values if I wish to visualize tract segments significant at 0.05.Thank you very much for your help,cheers,Cat ___ 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.
Re: [Freesurfer] dwi_motion Tracula
Dear Anastasia, With the new Tracula update installed, I ran the command: trac-all –qa –c dmrirc_file with location of bval specified and received the following error after ‘Loading volume-to-baseline affine transformations’ Could not open ../dmri/ dwi.ecclog for reading. It seems like all subjects do have the dwi.ecclog in their /dmri/ directories. Any ideas of what might have gone wrong? Cheers, Cat On Monday, July 21, 2014 1:53 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Cat - Just install the update and run trac-all -qa. This will produce the motion measures. Check the tutorial for where to find the output. a.y On Mon, 21 Jul 2014, Cat Chong wrote: Hello Anastasia, I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now, I would like to use the command dwi_motion on my data. I have installed the updates, but will I have to completely reprocess my data inducing steps trac-all -prep, trace-all -bedp, and trac-all path in order to use dwi_motion? cheers, Cat ___ 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 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] Tracula trac-all -stat flag -stat unrecognized
Hello Anastasia, I have just converted pathstas.overall.txt files to a table for group analyses. Now, I am trying to convert pathstats.byvoxel.txt files to a table for group analyses using the command: trac-all -stat -c I am receiving the error message: ERROR: flag -stat unrecognized I am working on a mac using bash script using Freesurfer version 5.3 Do you have any ideas? Cheers, Cat___ 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] Tracula AD weighted average
Dear Anastasia, Another quick question: We found significant differences in two subject groups for the AD_AVG as well as the AD_AVG_Weight, which is stated as the weighted average over the entire path distribution'. Could you tell me how the average weight is calculated and why it would be better to use than the AD_AVG perhaps? Thank you very much, Cat___ 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.
Re: [Freesurfer] Tracula trac-all -stat flag -stat unrecognized
Thanks Chris, I will try that right now! On Jul 18, 2014, at 2:37 PM, Chris Watson christopher.wat...@childrens.harvard.edu wrote: Do you have the latest version of Tracula? There was an update posted after FS 5.3 came out. On 07/18/2014 04:48 PM, Cat Chong wrote: Hello Anastasia, I have just converted pathstas.overall.txt files to a table for group analyses. Now, I am trying to convert pathstats.byvoxel.txt files to a table for group analyses using the command: trac-all -stat -c I am receiving the error message: ERROR: flag -stat unrecognized I am working on a mac using bash script using Freesurfer version 5.3 Do you have any ideas? Cheers, Cat ___ 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 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 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] Monte-Carlo Cluster Correction
Dear Experts, I was wondering if you could possibly help me with a reviewer-related question: We conducted a between-group-analysis estimating the interaction between cortical thickness and age. In summary, we wanted to investigate whether the interaction between cortical thickness and age is stronger for one group relative to another (using a DODS design). We cluster-corrected our results using a Monte Carlo cluster correction of p0.01 and attained significant group differences for several areas over the left and right hemisphere. One of the reviewer commented that although group differences were estimated for each hemisphere separately, they ought to have been cluster-corrected for both hemispheres. Would you be able to tell me whether or not cluster-correcting for both hemispheres is a necessity, or help me understand the possible implications of not having cluster-corrected for both hemispheres? Very Best Regards, Catherine___ 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] nuisance variable in qdec
Dear Doug, Thank you for your instantaneous response! Correcting for disease burden was actually a reviewer comment. We calculated mean cortical thickness estimates for regions that showed vertex-wise age-related cortical thickness differences between groups (using qdec) and then graphed out the slope aging-patterns between normal controls and patients, by extracting the data into SPSS. Basically, our findings indicated that for selected regions, the patients showed a steeper age-related decline. It was suggested by the reviewer to correct the correlation between age and cortical thickness for disease burden in the patient group (using partial correlations in SPSS). Would this be an alternative way? It would sure safe us from re-running our data:) Very Best Regards, Catherine___ 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] tracula bvec flipped sign
Dear Experts, I was hoping you could help me with the following problem. Tracula failed when I attempted to use Siemens (Skyra) dicoms as input for the configuration file, so I converted the dicoms to niftii format using dcm2nii. I used the gradient information of the bvec file created by dcm2nii ( after re-assembling it into the appropriate 3 column format) and specified it as the bvec.txt file to run Tracula. All post- processing worked fine and the fiber paths look ‘ok’ as far as I can tell. Here is the conundrum: When I compared the bvec gradients from the dcm2nii conversion to the SIEMENS hardwired protocol, the sign of the ‘z’ direction appears to have been flipped? I am not sure why this happened and whether to choose the “hardwired” Siemens scanner bvecs or the ones created by the niftii conversion. Which ones are correct to use? Very best regards, Catherine___ 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] Siemens dicom error on mri_convert
Hello Experts, I am trying to run the mri_convert command prior to the recon-all command on Siemens T1 dicoms (as suggested in the archives). I am using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X Lion 10.7.5 I am using the command below: mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz Below is the command line error I receive, it is a similar error I receive when I try to use the command recon-all on the Siemens dicoms. I have used freesurfer before on GE dicoms and never had a problem running recon-all. Is this error message particular to the Siemens dicoms, and would you be able to tell me how to proceed? Thank you very much for you help, Cat reading from 1002/IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 130 files in 1002 INFO: Scanning for Series Number 2 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName 1002/IM-0001-0001.dcm Identification NumarisVer syngo MR D11 ScannerModel Skyra PatientName RS-FMRI^RS-FMRI Date and time StudyDate 20130222 StudyTime 082109.14 SeriesTime 082812.906000 AcqTime 082237.315000 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol SAG MP Rage PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.03 InversionTime 1000 RepetitionTime 2400 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 128 SliceArraylSize 0 IsMosaic 1 ImgPos -78.6002 128. 93.1332 VolRes 1. 1. 1.2500 VolDim 0 0 0 Vc -0. -1. 0. Vr -0. -0. -1. Vs 0. 0. 0. VolCenter 0. 0. 0. TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header___ 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.
Re: [Freesurfer] Siemens dicom error on mri_convert
Dear Doug Yes, the data is straight off the scanner, I don't think it has been manipulated, but I will check. When I run the the command suggested I get the below error message: mri_convert –it dicom -ot mgz 1002/IM-0001-0001.dcm 1002.mgz mri_convert –it dicom -ot mgz 1002/IM-0001-0001.dcm 1002.mgz mri_convert: extra arguments (1002/IM-0001-0001.dcm and following) type mri_convert -u for usage I am not quite sure where I am making an error. Cat From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Cat Chong cavecreekcut...@yahoo.com; Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 23, 2013 10:06 AM Subject: Re: [Freesurfer] Siemens dicom error on mri_convert Is it straight off the scanner? It does not have the siemens ascii header which usually means that it has been manipulated in some way. You can try using mri_convert with --it dicom doug On 05/23/2013 12:57 PM, Cat Chong wrote: no it has not. *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, May 23, 2013 9:43 AM *Subject:* Re: [Freesurfer] Siemens dicom error on mri_convert has this file been anonymized? On 05/23/2013 12:39 PM, Cat Chong wrote: Hello Experts, I am trying to run the mri_convert command prior to the recon-all command on Siemens T1 dicoms (as suggested in the archives). I am using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X Lion 10.7.5 I am using the command below: mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz Below is the command line error I receive, it is a similar error I receive when I try to use the command recon-all on the Siemens dicoms. I have used freesurfer before on GE dicoms and never had a problem running recon-all. Is this error message particular to the Siemens dicoms, and would you be able to tell me how to proceed? Thank you very much for you help, Cat reading from 1002/IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 130 files in 1002 INFO: Scanning for Series Number 2 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName 1002/IM-0001-0001.dcm Identification NumarisVer syngo MR D11 ScannerModel Skyra PatientName RS-FMRI^RS-FMRI Date and time StudyDate 20130222 StudyTime 082109.14 SeriesTime 082812.906000 AcqTime 082237.315000 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol SAG MP Rage PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.03 InversionTime 1000 RepetitionTime 2400 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 128 SliceArraylSize 0 IsMosaic 1 ImgPos -78.6002 128. 93.1332 VolRes 1. 1. 1.2500 VolDim 0 0 0 Vc -0. -1. 0. Vr -0. -0. -1. Vs 0. 0. 0. VolCenter 0. 0. 0. TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
[Freesurfer] recon-all failed with errors
Dear Experts, I am able to to initiate recon-all but it fails at various stages during the recon-all process even though I should have plenty memory available to run the process. This is the error message I am getting and below is the log file. I am using the freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac OSX Lion 10.7.5 INFO: extension is mgz # #@# Talairach Thu May 23 14:05:55 MST 2013 /home/m117348/Documents/Schwedt_MRI/1004_out/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s 1004_out exited with ERRORS at Thu May 23 14:06:26 MST 2013 - FREESURFER_HOME /Applications/freesurfer/ Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 1987M wired, 5293M active, 2487M inactive, 9767M used, 22G free. program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id:
[Freesurfer] tracula batch processing
Hello Experts, Unfortunately I am currently only able to run tracula on a personal computer, System Version: Mac OS X 10.6.7 (10J869) Kernel Version: Darwin 10.7.0. I have no problem running a single subject on the dmrirc_single subject configuration file. When I try to run several subjects as described in the configuration file on the tracula tutorial page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula it finishes without errors but only the first subject gets processed. Do you have any ideas of what I am doing wrong? cheers, Cat___ 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] tracula longitudinal
Hello Experts, Please forgive another question. I have run 59 people through the recon-all freesurfer longitudinal stream with 2 timepoints (tp1id, tp2id). I want to run these subjects through tracula next, since the same people also received repeated Tensor imaging. To process everybody through tracula, I would use each person's original (cross-sectional) recon-all output and not the template or -long recon-all output, correct? Best regards, Catherine ___ 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] tracula bedpostx failure
Hello Experts, I am running bedpost x through fsl on the dmri directory (as advised in a previous post). I receive the fsl error message: “child process exited abnormally”. The command line error states: switching from /8000_tracula/8000_tracula_out/8005_DTI/dmri to /8000_tracula/8000_tracula_out/8005_DTI bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 /Applications/fsl/bin/bedpostx /8000_tracula/8000_tracula_out/8005_DTI/dmri -n 2 -w 1 -b 1000 subjectdir is /8000_tracula/8000_tracula_out/8005_DTI/dmri /8000_tracula/8000_tracula_out/8005_DTI/dmri/data not found All the output files of the trac-all -prep stage are there, but could I have made a mistake on my configuration file? I have attached it. Thank you very much for your help, Cheers, Cat dmrirc_single_subject Description: Binary data ___ 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] Tracula error? set: Variable name must begin with a letter
Hello Experts: I am running the first pre-processing step in Tracula and come across the error: set: Variable name must begin with a letter. Below is an excerpt of the script which seems to be running fine. Did I make a mistake in my dmrirc_single_subject file? Cheers, Catherine fmris-mac-pro-2:8000_tracula fmri$ trac-all -prep -c $SUBJECTS_DIR/dmrirc_single_subject set: Variable name must begin with a letter. INFO: SUBJECTS_DIR is /8000_tracula/ INFO: Diffusion root is /8000_tracula//8000_tracula_out/ Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /8000_tracula//8000_tracula_out//8001_DTI/scripts/dmrirc.local -log /8000_tracula//8000_tracula_out//8001_DTI/scripts/trac-all.log -cmd /8000_tracula//8000_tracula_out//8001_DTI/scripts/trac-all.cmd #- /Applications/freesurfer//bin/trac-preproc #- #@# Image corrections Mon Jan 14 09:37:29 MST 2013 mri_convert /8000_tracula//8001_DTI/IM-0006-0001.dcm /8000_tracula//8000_tracula_out//8001_DTI/dmri/dwi_orig.nii.gz mri_convert /8000_tracula//8001_DTI/IM-0006-0001.dcm /8000_tracula//8000_tracula_out//8001_DTI/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /8000_tracula//8001_DTI/IM-0006-0001.dcm... Starting DICOMRead2() dcmfile = /8000_tracula//8001_DTI/IM-0006-0001.dcm dcmdir = /8000_tracula//8001_DTI Ref Series No = 6 the script continues to run ok. ___ 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] Tracula problems initializing pathway
Hello Experts I am still at the first pre-proc step for Tracula and although the script is running, it seems to have difficulty initializing the first pathway (1 out of 18) Please see below script excerpt: Is that normal that it takes this many trials to initiate a pathway? Cheers, Catherine WARN: Could not find satisfactory control point fit - try 171 Finding center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 111 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 96 100 30 106 108 58 116 109 87 113 102 115 108 105 146 INFO: Distances between consecutive points are 31 31 29 32 WARN: Could not find satisfactory control point fit - try 172 Finding center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 107 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels___ 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] freeview tracula error
Dear Experts: I have worked my way through Tracula and things seem to work fine, but when I try to view my tractography outputs I get the following persistent error using freeview (copied below). I am using a Mac OS X 10.6.7. freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Could this be a similar problem as described below? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22110.html And if so, would this be a similar fix? Cheers, cat Below is the error message I get: freeview -v $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dmri/dtifit_FA.nii.gz \ $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dpath/5cpts/priormni/seg14/initmni/regflt/lh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' \ $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dpath/5cpts/priormni/seg14/initmni/regflt/rh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' [1] 24711 fmris-Mac-Pro-2:8000_tracula fmri$ 2012-08-29 12:51:30.566 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.571 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.593 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.596 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.616 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.619 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.640 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.643 freeview.bin[24711:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool))___ 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.
Re: [Freesurfer] freeview tracula error
Thank you for the almost immediate reply. Yes, it seems to be otherwise working, cheers, Cat From: Nick Schmansky ni...@nmr.mgh.harvard.edu To: Cat Chong cavecreekcut...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 29, 2012 2:35 PM Subject: Re: [Freesurfer] freeview tracula error does freeview otherwise appear to be working? that is, does it crash? the 'invalid drawable' messages can be ignored on the mac. n. On Wed, 2012-08-29 at 14:29 -0700, Cat Chong wrote: Dear Experts: I have worked my way through Tracula and things seem to work fine, but when I try to view my tractography outputs I get the following persistent error using freeview (copied below). I am using a Mac OS X 10.6.7. freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Could this be a similar problem as described below? http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22110.html And if so, would this be a similar fix? Cheers, cat Below is the error message I get: freeview -v $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dmri/dtifit_FA.nii.gz \ $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dpath/5cpts/priormni/seg14/initmni/regflt/lh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' \ $SUBJECTS_DIR/8000_tracula_out/8004_DTI/dpath/5cpts/priormni/seg14/initmni/regflt/rh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' [1] 24711 fmris-Mac-Pro-2:8000_tracula fmri$ 2012-08-29 12:51:30.566 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.571 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.593 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.596 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.616 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.619 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.640 freeview.bin[24711:907] invalid drawable 2012-08-29 12:51:30.643 freeview.bin[24711:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) ___ 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 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] tracula-snowleopard updates
Hello Experts, Just a quick question: Do the Tracula updates(dmri_mergepaths, etc) for snow_leopard replace the 'old' ones in freesurfer's bin directory? cheers, Cat ___ 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] tracula trac-all error malloc_error_break
Hello Experts, I get the following error when running trac-all: *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice I am using the update for trac-all that was recommended, but it still isn't working. I would be grateful for any suggestions. cheers, cat below is the trac-all log: Loading cortex mask from /Applications/freesurfer//trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(78737) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 13th slice Cannot allocate memory Darwin fmris-Mac-Pro-2.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:16:10 PST 2011; root:xnu-1504.9.37~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Aug 24 15:37:39 MST 2012___ 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] pial edit question
Dear Experts, I am occasionally noticing some 'pinching' on the inflated brain surfaces around the temporal lobe pole. When I check the brainmask.mgz files, the raised areas are due to a 'bubble' of pial surface forming on top of pial surface. Upon checking white matter and grey matter boundaries, the pial surface should really not be separated as a bubble, but should in fact be all one surface. What would you suggest would be the best way to fix this? The white matter seems to be fine. Best Regards, Catherine ___ 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] ROI labels
Dear Freesurfers, I would like to show several ROI labels that we created on top of an an average brain which demonstrates the group results of cortical thinning with advancing age. In qdec, when I go into FileLoad Label, I can only view one label at a time. Is there a way to show several labels together on an average brain, just for visualization purposes? cheers, Cat ___ 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] qdec group analysis
Hello Freesurfers, I have created an ROI label for 80 subjects in qdec. My question is the following: Is there a command that will create a .stats file for all my subjects rather than using the below command on each person individually? mris_anatomical_stats -l rh.ento.label \ -t rh.thickness -b -f 4000/stats/rh.ento.stats 4000 rh best regards, Cat___ 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] longitudinal analysis 5.0 or 5.1?
Dear Freesurfers: We have a large group of subjects (for which we have two time-points) that were run through the recon-all stream using 5.0. We have done no manual editing yet. We would like to do a longitudinal analysis of these subjects using 5.1 by comparing both time-points for each subject. Is that a possibility using 5.1? Also, at what point should I correct for topographical defects, or make edits to the white matter or brain mask volume? Should I edit both time-points separately first and then initiate the longitudinal analysis? If so, could I do the manual editing using 5.1? thank you very much for your help, cheers, cat___ 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] qdec and analysis results
Hello Experts, I am analyzing cortical thickness of two groups (APOE 4carries vs. noncarriers) in freesurfer with age as a co-variate. I am uncertain about the statistical differences behind: 1)Does the correlation between thickness and age accounting for APOE, differ from 0? in contrast to: 2)Does the thickness-age correlation differ between 1 and 0? I get significant results after FDR correction for the first but not for the second analysis. thank you for your help, catherine ___ 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.
Re: [Freesurfer] qdec analysis
Hi Doug, I spoke too soon. I tried to follow your advice and run either command: In a terminal, cd to the GLM directory inside qdec directory and then cd to the folder of the contrast of interest and run mri_segstats --id 1 --slabel fsaverage lh yourlabel --i gamma.mgh --sum yourlabel.sum the output yourlabel.sum will have information about the label including the mean gamma (gamma is a map of the contrast values). Along those same lines, you can run mri_segstats --id 1 --slabel fsaverage lh yourlabel --i y.mgh --avgwf yourlabel.dat y.mgh should be there already and is a stack of thickness maps for all your subjects the output yourlabel.dat will be a single column with the average thicknesses for each subject . however the error message I receive is that y.mgh could not be opened...and I also don't seem to have a gamma.mgh file? Here is the error message, I received: mri_segstats --id 1 --slabel fsaverage lh lh.Temporal_lobe.label --i y.mgh --avgwf lh.Temporal_lobe.label.dat sysname Darwin hostname fmris-Mac-Pro-2.local machine x86_64 user fmri Constructing seg from label Loading y.mgh mghRead(/8000_series/8000_series/qdec/example_contrast/y.mgh , -1): could not open file. Filename extension must be .mgh, .mgh.gz or .mgz ERROR: loading y.mgh fmris-Mac-Pro-2:example_contrast fmri$ ls X.mat lh-Avg-Intercept-thickness qdec.fsgd Xg.dat lh-Avg-thickness-Age-Cor rstd.mgh beta.mgh lh-Diff-1-0-Cor-thickness-Age rvar.mgh contrasts lh-Diff-1-0-Intercept-thickness sar1.mgh contrasts.sig.mgh lh.Temporal_lobe.label surface dof.dat lh.Temporal_lobe.label.dat y.fsgd error.log mask.mgh y.mgh fwhm.dat mri_glmfit.log thanks so much for your help: cat ___ 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] qdec and scatterplots
Hello Experts, I apologize for the basic question. I am currently examining the cortical thickness differences between two groups, contolling for age. On the scatterplot, I thought there was a way to view slopes and intercepts (between groups)? I can't however, figure out a way to get these trendlines to show up. best regards, and Happy Chinese New Year Catherine___ 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] qdec analysis
Hello Experts: In qdec, I would like to analyze if the thickness- entorhinal volume correlation differs between APOE positive and negative subjects accounting for age. I have chosen age as a nuisance variable and entorhinal volume as a covartiate. ( hope this is correct) Results show me several clusters of group differences following FDR correction. Here is my question: I would like to know what the mean value differences are between the groups for various clusters. And I would also like to know which group shows less of a correlation for certain clusters. Could you tell me where I would find those values? Best Regards, Catherine___ 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.
Re: [Freesurfer] SPGR compressed files
Hi Bruce, We want to analyze some scans that were compressed when they were stored. Compression factor varies from 3:1 to about 7:1 or so. unfortunately, we don't have access to the raw dicom data. Can we do this? thanks for your help, cheers, catherine From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Cat Chong cavecreekcut...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Friday, January 6, 2012 9:11 AM Subject: Re: [Freesurfer] SPGR compressed files Hi Catherine can you explain what you mean by compression? Bruce On Fri, 6 Jan 2012, Cat Chong wrote: Hi Experts, We wanted to run clinical scans that underwent some compression at the scanner through freesurfer. I just wanted to seek confirmation that SPGR sequences that have undergone slight compression can not be run through freesurfer, is that correct? thank you, catherine 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 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] SPGR compressed files
Hi Experts, We wanted to run clinical scans that underwent some compression at the scanner through freesurfer. I just wanted to seek confirmation that SPGR sequences that have undergone slight compression can not be run through freesurfer, is that correct? thank you, catherine ___ 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] QDEC:/ problems with generating stats Data Tables
HI Experts: Using Qdec, I have tried to generate Stats Data Tables, but below is the error message I received. .I get this error message for all subjects but the aseg.stats files are there and seem ok... any ideas of what I am doing wrong? cheers, catherine asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out SUBJECTS_DIR : /5000_series/5000_series Parsing the .stats files ERROR: The stats file /5000_series/5000_series/5002_out/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats file___ 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] SPGR gadolinium contrast
Hello Experts: Is is possible to run 3D SPGR's with contrast (gadolineum) through freesurfer? Also, in a separate dataset, we have 3D SPGR's that have unfortunately been compressed. Can they still be run? Thanks, catherine___ 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] Qdec: problems
Hi Experts: Sorry, I forgot to attach the following error message I get when I attempt to generate stats data tables: I would be grateful if you tell me what I am doing wrong, catherine asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out SUBJECTS_DIR : /5000_series/5000_series Parsing the .stats files ERROR: The stats file /5000_series/5000_series/5002_out/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files fmris-Mac-Pro-2:qdec fmri$ ERROR: In /usr/pubsw/packages/KWWidgets/CVS-7Aug2010/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x588e8d0): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out while executing vtkTemp2 GenerateStatsDataTables___ 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 Courses
Hi all, Just checking.. is the Freesurfer course in New Zealand this May the only course offered this year, or are there others? would love to go but New Zealand may be a stretch... cheers, catherine ___ 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] tracula and corona radiata
Hello Experts, I would like to be able to get measurements of the anterior portion of the corona radiata using tracula. Is this a possibility? I did not see it as an option in paths to reconstruct. thank you very much for your help, catherine___ 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] entorhinal cortex volume question
Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine___ 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] entorhinal cortex volume
Another basic question: Could you tell me what is the best way of putting the ?h.entorhinal_exvivo.stats into a spreadsheet for all subjects? Is there a way to achieve a textfile output for all subjects similar in concept to kvlQuantifyHippocampalSubfieldSegmentations.sh ? catherine___ 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] SPGR orientation
Hello Experts: I am new to Freesurfer. Does the SPGR data have to be of axial LPI orientation in order to run through recon all? thank you, cat ___ 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.
