Re: [Freesurfer] Tracula preprocessing step error
Hi I add the same problem; It finally worked : - using libreoffice instead of excel to transpose the bvec/bval files ; - with english as linguisitic parameter, - save the file as cvs document, with the filter parameters box checked - in the filer option choose "space" as field separator; " as text separator, "unicode UTF-8" as encoding cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours http://www.u930.tours.inserm.fr/ Service de Neurochirurgie et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 - Mail original - > De: "Anastasia Yendiki" > À: "Allison Gruber" > Cc: Freesurfer@nmr.mgh.harvard.edu > Envoyé: Mercredi 9 Janvier 2013 22:43:01 > Objet: Re: [Freesurfer] Tracula preprocessing step error > > > Hi Allison - Instead of using excel, I would use a unix-based text > editor, > whichever is available on the system where you are running the > analyses. > This way you can ensure that unix commands read your text files > properly. > > The 3 values for each diffusion gradient vector are its x, y, z > components, so I wouldn't change their order, unless you have reason > to > believe that the order is not correct the way it was given to you. > > Hope this helps, > a.y > > On Wed, 9 Jan 2013, Allison Gruber wrote: > > > Hi Anastasia, > > > > Thanks so much for your help. I was able to correct this problem in > > my > > configuration file. I have now run into another error- "bvecs and > > bvals don't have the same number of entries." I have read other > > postings about this error and can see that my bvec file is not > > formatted correctly when I import into Excel. However, I am not > > sure > > how to correctly fix this formatting. I know that I have 28 bval > > entries and > > 84 bvec entries, so the overall number is correct. I am just > > unclear on how > > to fix the formatting of the bvec file so that it corresponds > > correctly to > > the ordering in the bval file (which order the bvec entries should > > appear in > > within the three columns). Do you have any resources on this? > > > > Thank you again for your help, > > Allison > > > > Quoting Anastasia Yendiki : > > > >> > >> Hi Allison - The mri_convert command at the top of your log file > >> is > >> trying to convert the directory > >> /Users/Desktop/Tracula/diffusion_DTI to > >> a nifti file. From the name of that nifti file, it looks like it's > >> expecting to find a field map and not finding it. > >> > >> Hope this helps, > >> a.y > >> > >> On Tue, 8 Jan 2013, Allison Gruber wrote: > >> > >> > Dear Freesurfer experts, > >> > > >> > I have encountered the following error while running the tracula > >> > pre-processing command and was hoping you could help me > >> > understand how > >> > to correct this. > >> > > >> > Selection from log: > >> > > >> > mri_convert /Users/Desktop/Tracula/diffusion_DTI/ > >> > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz > >> > mri_convert /Users/Desktop/Tracula/diffusion_DTI/ > >> > /Users/Desktop/Tracula/diffusion_DTI/SubjectX/dmri/b0mag.nii.gz > >> > corRead(): can't open file > >> > /Users/Desktop/Tracula/diffusion_DTI/COR-.info > >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > >> > reading from /Users/Desktop/Tracula/diffusion_DTI/... > >> > Darwin MacBook-Pro.local 11.4.0 Darwin Kernel Version 11.4.0: > >> > Mon Apr > >> > 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 > >> > > >> > trac-preproc exited with ERRORS at Tue Jan 8 14:34:39 EST 2013 > >> > > >> > Please let me know if this is not enough information. Thank you > >> > for > >> > your help. > >> > > >> > Allison > >> > ___ > >> > 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu
Re: [Freesurfer] freesurfer question
Hi Catherine can you clarify? Are you getting them properly segmented in the aseg? Is this a disease population? There are a bunch of things going on in the images you sent, although it's hard to be sure from a single slice. It looks like your bandwidth is low enough that you are getting a lot of signal pileup in temporal regions. There also appear to be cortical lesions. Bruce On Thu, 10 Jan 2013, Catherine Bois wrote: > Ps. I have attached a few screenshots of the problem we are experiencing, to > clarify. We are also getting large areas of hyper-intensive white matter too. > > > Quoting Bruce Fischl on Wed, 9 Jan 2013 08:52:08 > -0500 (EST): > >> Hi Catherine >> >> what version are you running? We have a fix in 5.2 that helps this problem. >> It's not quite out yet, but you could download a beta if you want >> >> cheers >> Bruce >> >> On Wed, 9 Jan 2013, Catherine Bois wrote: >> >>> Hi, >>> >>> I am currently editing some scans (ie adding control points etc), >>> however I keep finding that after the editing often the brains look >>> "worse" than they did before; especially the medial temporal lobe >>> area. I have taken care not to put too many control points in/made >>> sure not to place them in partial volume areas, and only in areas that >>> are clearly excluded white matter. This problem has happened >>> repeatedly, yet looking at scans that my colleagues have edited (some >>> with up to 2000 control points) this problem does not occur. Has this >>> happened before, is it the software "malfunctioning" in some way? >>> >>> Thank you very much for your reply, >>> >>> >>> >>> >> >> >> 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
Re: [Freesurfer] QA Tools Snaps Scrambled - Follow up
Hi Louis- I dug a little deeper and examined the rgb files before conversion. The problem is not with the IM conversion, it is with the capture. For example, '_curv_lh_lat.rgb' is just fine, but from the same subject 'snapshot-talairach-H-128.rgb' is garbage. Any ideas on this? Thanks, Wil -Original Message- From: Irwin, William Sent: Wednesday, January 09, 2013 6:22 AM To: Louis Nicholas Vinke Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled - Clairification Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having problems with any of the other apps running on my system. Obviously I'm not asking you to help diagnose the health of my system, but though you might have some thoughts/suggestions. Regards, Wil -Original Message- From: Irwin, William Sent: Wednesday, January 09, 2013 5:37 AM To: Louis Nicholas Vinke Cc: freesurfer@nmr.mgh.harvard.edu; Irwin, William Subject: RE: [Freesurfer] QA Tools Snaps Scrambled Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-contained. This is a real mystery -Wil -Original Message- From: Louis Nicholas Vinke [mailto:vi...@nmr.mgh.harvard.edu] Sent: Tuesday, January 08, 2013 6:29 PM To: Irwin, William Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] QA Tools Snaps Scrambled Hi Irwin, It sounds like the snapshots from tksurfer are fine, but the ones from tkmedit are not being generated properly. It may be this peculiar bug where ImageMagick has trouble reading rgb files. Try converting an rgb file to a jpg 'convert file.rgb file.jpg'. You may get the error 'Improper image header'. The tksurfer tcl script saves tiff files, the tkmedit tcl script saves rgbs, which may explain why some images are fine. -Louis On Tue, 8 Jan 2013, Irwin, William wrote: > > Hi- > > > > I’ve come across a peculiar behavior with recon_checker, and am hoping > someone can shed some light on this. > > > > I have used it 100’s of times in the past, but not for about 2 months. > I recently processed a large set of cases I wanted to QC. When I ran > it, some, but not all, of the snaps were corrupted. Specifically the > talairach, aseg, surfs, and all the ‘detailed snaps’, which are > basically additional instances of the aforementioned types. The > inflated, curv, and parc are all just fine. As the process runs, all > images are being displayed in the pop-up windows, and the html page is > created. > > > > While there have been no system changes which should affect this, I > upgraded from ImageMagick 6.5.4 to 6.8.1 to see if this would fix the > problem. The problem remains. And the problem remains w/ or w/o the > flag for detailed snaps. > > > > If all of the images were corrupted, I would have certainly concluded > something has gone awry with my system. The fact that only some of the > images are corrupted makes me scratch my head. > > > > Thoughts? Suggestions? > > > > Thanks, > > Wil > > > 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
Re: [Freesurfer] FreeSurfer problem on VirtualBox Linux
Unfortunately Windows XP SP3 is no longer Tier-1 supported for VirtualBox. I suggest you to try it on Windows 7 or Windows 8. cheers PPJ - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Jan 9, 2013 at 7:49 PM, Nick Schmansky wrote: > Carissa, > > Unfortunately I dont think we can help with this problem, as we > currently do not have the resources to support the Windows VM instance. > However, an alternative that has worked for others is to do the > following: install the FSL Windows VM, described here: > > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows > > once that is up-and-running, then within that linux instance, just > download and install our linux centos 4 freesurfer build. this also > means you can update to v5.2 when that is released in a couple weeks. > > Nick > > > On Wed, 2013-01-09 at 08:34 +, Carissa Nadia Kuswanto (IMH) wrote: > > Hi there, > > > > > > > > My operating system is Windows XP SP3 and it has been loaded with > > VirtualBox 4.2.6 for Windows hosts and we would like to run > > freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi. But when > > we attempt to launch FreeSurfer, the terminal seems to hang with the > > following message: > > > > > > > > GRUB loading stage 1.5 > > > > GRUB loading, please wait... > > > > > > > > Would you kindly help us on how to overcome this problem? I thank you > > in advance for your kind attention. > > > > > > > > Best regards, > > > > Carissa > > > > > > > > __ > > The information contained in this e-mail and the attachments (if any) > > may be privileged and confidential and is intended solely for the > > named addressee. If you are not the intended recipient, please do not > > print, retain copy, disseminate, distribute, or use this e-mail or any > > part thereof. Please notify the sender immediately by replying to this > > e-mail and delete all copies of this e-mail and the attachments. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > 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] Fwd: Problems in testing out newly installed Freesurfer with autorecon-1 option
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 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 >
[Freesurfer] reversing recon-all resampling
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 ___ 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] recon-all error
Does the disk have space on it? It could also be a virtualbox problem,
in which case I'll leave it for others.
doug
On 1/10/13 8:29 PM, ZhiLiangLong wrote:
Hi everyone:
I am using freesurfer 5.1.0 to run my own data to compute
cortical thickness in VirtualBox. When it runs the command:
"mri_aparc2aseg --s chong_lan --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ", it got
errors("mghRead(/mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aparc+aseg.mgz):
could not read 262144 bytes at slice 184"). I have no idea how to
make it correct. I need help.
The detials are in the attachment.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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] reversing recon-all resampling
Hi Jeff, see if this page answers your question http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug On 1/10/13 6:24 PM, Jeff Eriksen wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
