Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

How to transform a ROI volume to dwi space?
by Ran Xu 24 Mar '13

24 Mar '13

Dear Freesurfer experts, I got the individual ROI volumes (not the surface) from aparc+aseg.nii.gz file, now I wanna use them as the seed regions in dwi space. I noticed that these ROIs are in the same space with "T1_brain", but this "T1_brain" is not the native T1. So could I register this T1_brain with the original T1, then applying transformation to these ROIs? Then, do registration between original T1 and dwi? All of registrations are linear or nonlinear? Thanks. Ran

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Merging PArcellation labels
by Anupa AV 24 Mar '13

24 Mar '13

Dear All, Can anyone tell me how to merge the parcellation labels using tksurfer.? For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and caudal middle frontal gyrus.

3 2

How to get an individual gray matter volume?
by Ran Xu 23 Mar '13

23 Mar '13

Dear Freesurfer experts, I used the Index from aseg.txt to get the left thalamus (Index 10), but the real volume I got is different from the size in aseg.txt. Its volume is 5007 in aseg.txt and I programmed a matlab code to find all values equaling to 10 in aparc+aseg.nii. However, the volume I got is 5237 from matlab code. Could you tell me how to extract the real ROI? I mean its volume number should be the same with the one in aseg.txt? Thanks.

2 1

R: Re: hippo subfield
by stdp82＠virgilio.it 23 Mar '13

23 Mar '13

Hi Zeke, as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. After rerunning I have: [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfieldsSubject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_provaActual FREESURFER_HOME /Applications/freesurfer-rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.logDarwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64#--------------------------------------------#@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff01side: leftinputDirectory: /Applications/freesurfer/subjects/subject_provaoutputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 22-mar-2013 20.53 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] hippo subfield Stefano, In order to fix this issue please follow these instruction exactly: 1) Download the file "kvl.zip" from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ 2) Overwrite the existing kvl files in /Application/freesurfer/bin with the files in kvl.zip I was able to replicate your issue and solve it using the steps above. If these steps do not solve the issue for you, please respond with a the exact error you receive. Hope this helps. -Zeke On 03/22/2013 12:00 PM, stdp82(a)virgilio.it wrote: > I'm running: > > recon-all -s Diff02 -hippo-subfields > > with the following error. > > Thanks. > > > Stefano > > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02 > Actual FREESURFER_HOME /Applications/freesurfer > -rw-rw-r-- 1 Stefano wheel 499999 Mar 22 16:53 > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 > #-------------------------------------------- > #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 > \n mkdir -p > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > \n kvlSegmentHippocampalSubfields.sh Diff02 left > /Applications/freesurfer/subjects/subject_prova/Diff02 > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > \n > Doing left side > meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz > compressionLookupTableFileName: > /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt > boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz > subjectName: Diff02 > side: left > inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02 > outputDirectory: > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults > directory > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 > already exists > directory > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > already exists > cd > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left > cp -f > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz . > cp -f > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz . > cp -f > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm > . > cp /Applications/freesurfer/data/GEMS/imageDump.mgz . > kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 > 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 > dyld: Library not loaded: libITKCommon.3.16.dylib > Referenced from: /Applications/freesurfer/bin/kvlApplyTransform > Reason: image not found > /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: > 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 > -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 > 0.9996 -3.1939 > *failed to do kvlApplyTransform imageDump.mgz > -0.9991 -0.0328 0.0258 144.0010 > -0.0330 0.9994 -0.0086 2.6560 > 0.0255 0.0094 0.9996 -3.1939* > *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun > Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64* > * > * > *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013* > > For more details, see the log file > /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

2 1

Brodmann area thickness, surface area and volume
by _andreia_＠sapo.pt 23 Mar '13

23 Mar '13

Hi all, I'm using FS 5.0 and some time ago I was told by Bruce that I had to threshold the BA in order to have an approximate area when overlaying in the inflated surface. To get surface area values I also need to use the label_area and put a threshold having the possibility to choose the surface that I want, either white or pial. But I can also get the BA stats in a table for all subjects and areas using either mris_anatomical_stats (on each label) or usinga script by Jamaan to get the table (since I already have the ?.BA.stats files), right? My question is, which is the better/correct way to get the thickness and surface area values of the BA to export for statistical analysis since there are the thresolds issue. I want to study mainly cortical thickness and surface area but also look also at the volume (which is surface-based, thus thickness*surface are will not be = volume since they are an average from each label, right?). I' not sure of which approach to follow now... Does it depend on the measure I'll be using? Thank you! Andreia

2 4

cortical recontruction error
by Claudia Dacquino 23 Mar '13

23 Mar '13

Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a problem with one subject, during the cortical reconstruction (recon-all) the process stops at this stage: mri_cc <http://surfer.nmr.mgh.harvard.edu/fswiki/mri_cc> -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> at this point: final transformation (x=128.0, yr=0.978, zr=0.153): 1.000 -0.003 0.017 -1.456; 0.003 1.000 0.000 8.654; -0.017 0.000 1.000 25.201; 0.000 0.000 0.000 1.000; without giving me any error message, it just stops. Do you have some ideas for why it happens? thanks to everyone, Claudia

2 1

Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology
by Bruce Fischl 23 Mar '13

23 Mar '13

p.s. I don't know why that option doesn't work - I didn't even realize it existed On Sat, 23 Mar 2013, falk.luese(a)gmx.net wrote: > Hi Bruce, > > well, there is an option called -correct_defect within > mris_fix_topology, which is meant to correct just one defect at a time. > However, after the defect is corrected one is getting a message like: > > ?TERMINATING AFTER CORRECTED DEFECT > > no such file or directory? > > I haven?t been able to figure out how to save this or if this is even > possible. Maybe I am missing the correct flag to do so. May it otherwise be > possible to remove certain defects from ?h.defect_labels or something > similar? > > The errors of the filled.mgz result in a faulty surface > reconstruction of ?h.orig.nofix and every following surface like ?h.white > and ?.pial in that area. Therefore I wanted to remove these in before and, > if possible, automatically. > > Best, > Falk > > Von: Bruce Fischl > Gesendet: ?22?. ?März? ?2013 ?19?:?14 > An: ""Falk Lüsebrink"" <falk.luese(a)gmx.net> > Cc: FreeSurfer > Betreff: Re: [Freesurfer] Two questions regarding mri_fill and > mris_fix_topology > > Hi Falk > > I don't think it's possible to fix just one defect, unless Florent > included some option that I am not aware of. > > I also wouldn't worry too much about the filled.mgz. Make sure that the > aseg.mgz and the ?h.white and ?h.pial are accurate > cheers > Bruce > On Fri, 22 Mar 2013, > "Falk Lüsebrink" wrote: > > > Dear FreeSurfers, > > > > I am processing some T1-weighted images of the human brain with an > isotropic resolution of .5 mm using version 5.1. > > > > After mri_fill my hemispheres are separated nicely and the cerebellum is > completely removed. However, looking at the filled.mgz, posterior and > > superior of the corpus callosum some residual of white matter can be found > in the longitudinal fissure. It does not remain if I look at the > > conformed data, altough these leftovers are found in the wm.mgz of both > datasets. As this does not happen using conformed data I assume that the > > cutting plane is not "broad" enough in case of higher resolution data or > something related. Is there some way to tweak this? > > > > Secondly, I currently skip the -fix stage of recon-all completely while > processing this data, but I would like to correct at least some of its > > defects. I already I have seen in the help of mris_fix_topology that it is > possible to fix just one defect and I extracted the defects and their > > number of vertices using the defect-seg script. Is it possible to save the > resulting surface, so I am able to correct the defects I want > > to consecutively? > > > > Best, > > Falk > > > > > >

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Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology
by Bruce Fischl 23 Mar '13

23 Mar '13

Hi Falk have you tracked down the source of the defect in the wm.mgz? Sometimes very minor edits can correct even major defects. If you are having trouble with this feel free to upload the dataset and one of us will take a look Bruce On Sat, 23 Mar 2013, falk.luese(a)gmx.net wrote: > Hi Bruce, > > well, there is an option called -correct_defect within > mris_fix_topology, which is meant to correct just one defect at a time. > However, after the defect is corrected one is getting a message like: > > ?TERMINATING AFTER CORRECTED DEFECT > > no such file or directory? > > I haven?t been able to figure out how to save this or if this is even > possible. Maybe I am missing the correct flag to do so. May it otherwise be > possible to remove certain defects from ?h.defect_labels or something > similar? > > The errors of the filled.mgz result in a faulty surface > reconstruction of ?h.orig.nofix and every following surface like ?h.white > and ?.pial in that area. Therefore I wanted to remove these in before and, > if possible, automatically. > > Best, > Falk > > Von: Bruce Fischl > Gesendet: ?22?. ?März? ?2013 ?19?:?14 > An: ""Falk Lüsebrink"" <falk.luese(a)gmx.net> > Cc: FreeSurfer > Betreff: Re: [Freesurfer] Two questions regarding mri_fill and > mris_fix_topology > > Hi Falk > > I don't think it's possible to fix just one defect, unless Florent > included some option that I am not aware of. > > I also wouldn't worry too much about the filled.mgz. Make sure that the > aseg.mgz and the ?h.white and ?h.pial are accurate > cheers > Bruce > On Fri, 22 Mar 2013, > "Falk Lüsebrink" wrote: > > > Dear FreeSurfers, > > > > I am processing some T1-weighted images of the human brain with an > isotropic resolution of .5 mm using version 5.1. > > > > After mri_fill my hemispheres are separated nicely and the cerebellum is > completely removed. However, looking at the filled.mgz, posterior and > > superior of the corpus callosum some residual of white matter can be found > in the longitudinal fissure. It does not remain if I look at the > > conformed data, altough these leftovers are found in the wm.mgz of both > datasets. As this does not happen using conformed data I assume that the > > cutting plane is not "broad" enough in case of higher resolution data or > something related. Is there some way to tweak this? > > > > Secondly, I currently skip the -fix stage of recon-all completely while > processing this data, but I would like to correct at least some of its > > defects. I already I have seen in the help of mris_fix_topology that it is > possible to fix just one defect and I extracted the defects and their > > number of vertices using the defect-seg script. Is it possible to save the > resulting surface, so I am able to correct the defects I want > > to consecutively? > > > > Best, > > Falk > > > > > >

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Two questions regarding mri_fill and mris_fix_topology
by "Falk Lüsebrink" 23 Mar '13

23 Mar '13

3 2

Re: [Freesurfer] trac-all -prep exited with errors
by Anastasia Yendiki 22 Mar '13

22 Mar '13

Hi Jon - You will have to email the list with specifics about your recon-all problem, including recon-all.log. I can't guess what the problem is with no other information. I recommend starting a different email thread about it. a.y On Fri, 22 Mar 2013, Jon Wieser wrote: > > there is not a aparc+aseg.mgz file in the freesurfer/mri directory. > strange. I ran recon-all autorecon1, autorecon2, and autorecon3 successfully and check the results. > they looked ok > Jon > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Friday, March 22, 2013 4:19:57 PM > Subject: Re: [Freesurfer] trac-all -prep exited with errors > > > It will, unless it doesn't find the anatomical segmentation of the subject > ($SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz). > > On Fri, 22 Mar 2013, Jon Wieser wrote: > >> I ran the flirt command on command line and got the same error. >> I noticed that the freesurfer/dlabel directory did not have an anatorig directory in it. >> I created this "anatorig" directory in the freesurfer/dlabel directory and ran the flirt command again. >> it ran ok. >> >> it created the /freesurfer/dlabel/anatorig/lowb_brain_mask.flt >> >> Is Trac-all supposed to create the freesurfer/dlabel/anatorig directory? >> >> >> I will try running trac-all again >> Jon >> >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Sent: Friday, March 22, 2013 2:23:10 PM >> Subject: Re: [Freesurfer] trac-all -prep exited with errors >> >> >> Can you run the flirt command that gives the error directly on the command >> line? >> >> On Fri, 22 Mar 2013, Jon Wieser wrote: >> >>> Hi Anastasia, >>> we have plenty of disk space, 386 GB >>> the file does not exist >>> >>> freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz >>> >>> the entire freesurfer directory has read,write, and executable permission >>> >>> Jon >>> >>> >>> ----- Original Message ----- >>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Sent: Friday, March 22, 2013 1:06:22 PM >>> Subject: Re: [Freesurfer] trac-all -prep exited with errors >>> >>> >>> Hi Jon - The error says that it can't open a file *for writing*. Any >>> chance it's a disk space issue or, if the file already exists, a >>> permission issue? >>> >>> a.y >>> >>> On Fri, 22 Mar 2013, Jon Wieser wrote: >>> >>>> HI Ansatasia >>>> I have attached the trac-all.log >>>> Jon >>>> >>>> ----- Original Message ----- >>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Sent: Friday, March 22, 2013 11:49:35 AM >>>> Subject: Re: [Freesurfer] trac-all -prep exited with errors >>>> >>>> >>>> Hi Jon - Can you please send all of trac-all.log? Sometimes there are >>>> hints earlier than where the error actually occurs. >>>> >>>> Thanks, >>>> a.y >>>> >>>> On Fri, 22 Mar 2013, Jon Wieser wrote: >>>> >>>>> Hi >>>>> I ran trac-all -prep -c dmrirc_single_subject >>>>> and got the following error: >>>>> >>>>> here's the end of the output from trac-all: >>>>> >>>>> >>>>> RegMat --------------------------- >>>>> 1.000 -0.016 -0.000 4.210; >>>>> 0.000 -0.005 1.000 2.417; >>>>> -0.016 -1.000 -0.005 0.018; >>>>> 0.000 0.000 0.000 1.000; >>>>> FSLOUTPUTTYPE NIFTI_GZ >>>>> tkreg2FSL: mov det = -64, ref det = -1 >>>>> Cleaning up >>>>> >>>>> Started at Fri Mar 22 11:35:44 CDT 2013 >>>>> Ended at Fri Mar 22 11:38:10 CDT 2013 >>>>> BBR-Run-Time-Sec 146 >>>>> >>>>> bbregister Done >>>>> To check results, run: >>>>> tkregister2 --mov /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/dwi.nii.gz --reg /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.dat --surf >>>>> >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.bbr.mat >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2diff.bbr.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2anatorig.mat >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2diff.bbr.mat >>>>> #------------------------------------- >>>>> #@# Inter-subject registration Fri Mar 22 11:38:10 CDT 2013 >>>>> flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_mni.nii.gz -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat -cost mutualinfo >>>>> >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anat.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.flt.mat >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.flt.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anat.bbr.mat >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2diff.bbr.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.bbr.mat >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat -concat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anat2mni.mat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2anat.mat >>>>> convert_xfm -omat /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/mni2anatorig.mat -inverse /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/anatorig2mni.mat >>>>> #------------------------------------- >>>>> #@# Masks Fri Mar 22 11:41:27 CDT 2013 >>>>> flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz -applyxfm -init /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2mni.flt.mat -interp nearestneighbour >>>>> flirt -in /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/diff/lowb_brain_mask.nii.gz -ref /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/brain_anat_orig.nii.gz -out /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz -applyxfm -init /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dmri/xfms/diff2anatorig.flt.mat -interp nearestneighbour >>>>> Error: failed to open file /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt.nii.gz >>>>> ERROR: Could not open image /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt >>>>> Image Exception : #23 :: Failed to open volume /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1267//freesurfer/dlabel/anatorig/lowb_brain_mask.flt for writing >>>>> terminate called after throwing an instance of 'RBD_COMMON::BaseException' >>>>> Abort >>>>> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >>>>> >>>>> trac-preproc exited with ERRORS at Fri Mar 22 11:41:39 CDT 2013 >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> 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. >>>> >>>> >>>> >>> >>> >> >> > >

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