Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

peculiar postop recon?
by Borzello, Mia 15 Jan '13

15 Jan '13

Hey Freesurfers, Hope all is well in the new year! I ran a reconstruction with a postop MRI and for some reason it looks like part of the frontal lobe is getting cut off. Based on the patient's postop report, I would expect to see a temporal lobectomy. Thanks so much, Mia

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error at ex-vivo entorhinal cortex label lh
by Terri Scott 15 Jan '13

15 Jan '13

Hello, I'm new to using freesurfer and I have gotten the following error when running recon-all on a new set of subjects. #@# Ex-vivo Entorhinal Cortex Label lh Tue Jan 15 09:25:23 EST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o KAN_adapt_02 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject KAN_adapt_02. processing subject lh.EC_average... MRIScomputeVertexSpacingStats: unsupported vertex set 0 eroding label 1 times before writing thresholding label stat at 0.400 before writing Linux mh21 2.6.38-16-generic #67-Ubuntu SMP Thu Sep 6 17:58:38 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s KAN_adapt_02 exited with ERRORS at Tue Jan 15 09:25:29 EST 2013 Everything seems to run fine up until this point. I need to run cvs on these subjects, will I need to re-run recon-all for cvs registration to work? Thanks, Terri

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reversing recon-all resampling
by Jeff Eriksen 15 Jan '13

15 Jan '13

I have been asked to use FreeSurfer to create a good brain mask for use in another analysis stream (DTI and other things). I have chosen to do this by running recon-all on the structural scan, then taking the (aseg+aparc) and using FSL to dilate and erode to fill holes. This I binarize and rotate back into the same orientation as the original structural volume, and finally strip the padding added by recon-all, thus making the mask match the original T1 so it can be overlaid properly. The only problem is that, besides rotating and padding, recon-all also resamples to exactly 1.0 isovoxel, whereas the original T1 was 1.0 x 1.0 x 1.1 mm. Thus, I need to find a way to undo this resampling. Best I can determine this happens in the recon-all stream near the beginning where is seems to create some Talariach transform. Any ideas how to undo this xform, or can you suggest a better way to accomplish my goal. -Jeff Eriksen

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Adding voxels
by Kristina Nalbandian 14 Jan '13

14 Jan '13

Hi can anyone give me some information on how I can add voxels. The gray matter that the arrow is pointing to was not included in the original recon-all -all and I was wondering if there was any way I could fix this problem during the editting. Thank you, Kristina Nalbandian

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recon-all 5.2 not generating surfaces
by Jonathan Holt 14 Jan '13

14 Jan '13

In 5.0.0 I was used to dealing with brainmask.mgz files. in 5.2.0, I have so far been able to generate a T1.mgz, which to my eyes, looks OK. However, the resulting surf folder is empty and I'm not sure why. Log file attached. jon

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FW: Freesurfer fails
by Franklin, Crystal G 14 Jan '13

14 Jan '13

On 1/14/13 11:38 AM, "Franklin, Crystal G" <FRANKLINC(a)uthscsa.edu> wrote: >I put the data on your ftp site in the folder called >crystal_failed_talairach.tar. > >Thanks, >Crystal > >On 1/14/13 9:31 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >>Hi Crystal >> >>we'll need the image volume also >> >>cheers >>Bruce >>On Mon, 14 Jan 2013, Franklin, Crystal G >>wrote: >> >>> Bruce, >>> >>> I have visually checked the transforms and they do indeed seem >>>incorrect. >>> The images are stretched. I have attached the talairach.xfm for one of >>> the images that failed and one that worked. >>> >>> Thanks for all your help, >>> Crystal >>> >>> On 1/13/13 3:08 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>>> can you cc the list? Have you visualized the transform to see if it is >>>> indeed incorrect? >>>> >>>> On Sun, 13 Jan 2013, Franklin, Crystal G wrote: >>>> >>>>> I used mri_convert to create the 001.mgz file. In freeview the >>>>> directions appear correct. >>>>> >>>>> Thanks, >>>>> Crystal >>>>> -----Original Message----- >>>>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>>>> Date: Sun, 13 Jan 2013 09:02:16 >>>>> To: Franklin, Crystal G<FRANKLINC(a)uthscsa.edu> >>>>> Cc: Freesurfer(a)nmr.mgh.harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] Freesurfer fails >>>>> >>>>> Hi Crystal >>>>> >>>>> how did you create the 001.mgz? When you view it in freeview does >>>>> freeview have the correct directions in the anatomy (i.e. I/S, A/P >>>>>and >>>>> L/R)? >>>>> >>>>> cheers >>>>> Bruce >>>>> On Sat, 12 Jan 2013, Franklin, Crystal G wrote: >>>>> >>>>>> Freesurfer, >>>>>> >>>>>> I have been running a group of subjects through recon-all and some >>>>>>of >>>>>> the >>>>>> subjects are failing at the very beginning of the process and I am >>>>>>not >>>>>> sure >>>>>> why. The images look fine, but I keep getting the following >>>>>>error: >>>>>> >>>>>> #@# Talairach Failure Detection Fri Dec 7 10:54:57 CST 2012 >>>>>> /Applications/freesurfer/subjects/PHY002/mri >>>>>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n >>>>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>>>>> ***FAILED*** (p=0.0013, pval=0.0000 < threshold=0.0050) >>>>>> INFO: Attempting MINC mritotal to perform Talairach align >>>>>> >>>>>> Do you know what could be causing this? >>>>>> >>>>>> I read that you can include the command ?notal ?check to skip this >>>>>> test, but how >>>>>> will this effect my data? If I run this command on the subjects >>>>>>that >>>>>> failed and combine their results with the subjects that worked will >>>>>>my >>>>>> group >>>>>> results be effected? >>>>>> >>>>>> Any help would be appreciated. I have attached one of the log files >>>>>> for a >>>>>> subject that failed. >>>>>> >>>>>> Thanks, >>>>>> Crystal >>>>>> >>>>>> >>>>> >>>>> >>>>> 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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Fwd: Problems in testing out newly installed Freesurfer with autorecon-1 option
by Susan Kuo 14 Jan '13

14 Jan '13

Thank you, Nick. I tried using fixup_mni_paths, but received a poor result. I copied the stdout below: *** yocto/j/dti7/Susie/freesurfer/subjects> su Password: root@yocto:/j/dti7/Susie/freesurfer/subjects# fixup_mni_paths fixup_mni_paths: command not found root@yocto:/j/dti7/Susie/freesurfer/subjects# cd $FREESURFER_HOME/bin root@yocto:/usr/local/freesurfer/bin# fixup_mni_paths fixup_mni_paths: command not found root@yocto:/usr/local/freesurfer/bin# ./fixup_mni_paths Using perl '/usr/bin/perl' Patching autocrop...(original file saved to autocrop.old) Patching field2imp...(original file saved to field2imp.old) Patching imp2field...(original file saved to imp2field.old) Patching make_template...(original file saved to make_template.old) Patching mritoself...(original file saved to mritoself.old) Patching mritotal...(original file saved to mritotal.old) Patching nu_correct...(original file saved to nu_correct.old) Patching nu_estimate...(original file saved to nu_estimate.old) Patching nu_estimate_np_and_em...(original file saved to nu_estimate_np_and_em.old) Patching nu_evaluate...(original file saved to nu_evaluate.old) Patching resample_labels...(original file saved to resample_labels.old) Patching sharpen_volume...(original file saved to sharpen_volume.old) Patching xfmtool...(original file saved to xfmtool.old) done. Here are the changes: diff autocrop autocrop.old diff field2imp field2imp.old diff imp2field imp2field.old diff make_template make_template.old diff mritoself mritoself.old diff mritotal mritotal.old diff nu_correct nu_correct.old diff nu_estimate nu_estimate.old diff nu_estimate_np_and_em nu_estimate_np_and_em.old diff nu_evaluate nu_evaluate.old diff resample_labels resample_labels.old diff sharpen_volume sharpen_volume.old diff xfmtool xfmtool.old done. Note: not all systems will require a patch, and may not show any differences. Now a test of the MNI tool 'nu_correct'... nu_correct: Command not found. A version number and usage message should have been displayed. *** I double-checked that /usr/bin/perl exists, so that's ok. I've been crawling the forums, but I can't find a good answer for what appears to be a simple problem. Can I fix this manually? Thanks! Susie On Wed, Jan 9, 2013 at 4:29 PM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>wrote: > Susan, > > there appear to be two problems here. the first and main problem is the > one: > > nu_correct: Command not found. > > nu_correct is a script which has as its first line: > > #!/usr/bin/perl -w > > so can you check that you have perl installed at /usr/bin/perl? > > better yet, run this script: > > fixup_mni_paths > > which does the checking for you and attempts to fix the scripts. > > the other problem appears to be the fact that mri_nu_correct.mni doesnt > exit upon finding the error that the files are missing. this is bad, > although in looking at the script, it ought to. the next release will > contain a double check. from the looks of your script, it appears that > you are running recon-all with a subject that had its data already > processed, so nu.mgz existed already, so it just used that and continued > on. so the results are correct (assuming nu.mgz was decent to begin > with), but resolving the nu_correct issue is the important thing to do. > > Nick > > > On Wed, 2013-01-09 at 11:00 -0500, Susan Kuo wrote: > > Hi, > > I'm currently in the process of verifying that my install of > > Freesurfer works. I have an Ubuntu 12.04.1 LTS box. I encountered what > > appeared to be 4 errors after running recon-all -s bert -autorecon1. > > The last line I included here states that the command completed > > without error, so I'm not sure if I should be concerned > > thatnu_correct wasn't found, or that there were loading errors, and > > a mincREAD() error. Could you help me identify what I need to do to > > correct these issues? I've included the standard output for this > > command as a text file here. There appear to be 4 issues: > > > > > > > > > > ***ISSUE 1: cannot find nu_correct ************************* > > nu_correct: Command not found. > > INFO: current FREESURFER_HOME does not match that of previous > > processing. > > > > > > ***ISSUE 2: No such file or directory error******************** > > cp: cannot stat `./tmp.mri_nu_correct.mni.25253/nu2.mnc': No such file > > or directory > > mri_binarize --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc --min -1 > > --o ./tmp.mri_nu_correct.mni.25253/ones.mgz > > mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc > > > > > > ***ISSUE 3: Loading error****************************** > > Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz > > ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz > > mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25253/ones.mgz > > --i ./tmp.mri_nu_correct.mni.25253/nu2.mnc > > --sum ./tmp.mri_nu_correct.mni.25253/sum.junk > > --avgwf ./tmp.mri_nu_correct.mni.25253/output.mean.dat > > mghRead(./tmp.mri_nu_correct.mni.25253/ones.mgz, -1): could not open > > file > > > > > > ***ISSUE 4: Loading error****************************** > > Loading ./tmp.mri_nu_correct.mni.25253/ones.mgz > > ERROR: loading ./tmp.mri_nu_correct.mni.25253/ones.mgz > > (standard_in) 1: syntax error > > mris_calc > > -o ./tmp.mri_nu_correct.mni.25253/nu2.mnc > ./tmp.mri_nu_correct.mni.25253/nu2.mnc mul > > mincRead(): can't find file ./tmp.mri_nu_correct.mni.25253/nu2.mnc > > > > > > ****This is the last line to standard output, and it seems > > reassuring********************** > > recon-all -s bert finished without error at Tue Jan 8 17:49:19 EST > > 2013 > > > > > > > > > > I appreciate whatever help you can give me, and thank you very much > > for your time! The attached is a text file. > > > > > > > > > > Best, > > S Kuo > > _______________________________________________ > > 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. >

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Tracula problems initializing pathway
by Cat Chong 14 Jan '13

14 Jan '13

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

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Re: [Freesurfer] Tracula error? set: Variable name must begin with a letter
by Anastasia Yendiki 14 Jan '13

14 Jan '13

Great, glad it works! On Mon, 14 Jan 2013, Cat Chong wrote: > Dear Anastasia, > > Thank you so much for your fast reply. I believe I found the pesky mistake > in my dmrirc file.. I omitted a space > in the last line > set ncpts =5 > once I fixed this to set ncpts = 5 and re-ran the command I no longer get > this error message. > Thank you very much, > Catherine > > > > ____________________________________________________________________________ > From: Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > To: Cat Chong <cavecreekcutter(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, January 14, 2013 10:04 AM > Subject: Re: [Freesurfer] Tracula error? set: Variable name must begin with > a letter > > > Hi Cat - Can you please send along your dmrirc file? It's hard to tell > without looking at it. > > a.y > > On Mon, 14 Jan 2013, Cat Chong wrote: > > > > > 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(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. > > > > >

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Tracula error? set: Variable name must begin with a letter
by Cat Chong 14 Jan '13

14 Jan '13

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.

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Freesurfer January 2013