Thanks. I just added it into our code, so new versions will not have this problem. doug
Maryam Vaziri Pashkam wrote: > Hi, > > Following up on the preprocessing error: > > Can't connect? tcp_connect[connect]: Connection timed out > > We figured where the problem is. This error came out when freesurfer > calls an afni function. Apparently it tries to check which version of > afni it is using against the internet to find out the most recent > version. Suppressing the afni version check solved the problem. I > just added this line to my .bashrc file: > export AFNI_VERSION_CHECK=NO > > Maryam > > On Mon, Dec 12, 2011 at 12:00 PM, > <freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> wrote: > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > <mailto:freesurfer-ow...@nmr.mgh.harvard.edu> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. preprocessing error (Maryam Vaziri Pashkam) > 2. Re: preprocessing error (Douglas Greve) > 3. convert surface label on to functional image (Zhangyuanchao) > 4. References/materials for interaction analysis in freesurfer > (Bhavani Shankara Bagepally) > 5. Re: dt_recon error (Yuko Yotsumoto) > 6. Re: dt_recon error (Yuko Yotsumoto) > 7. Re: run preproc-sess with -nomc (Thunell Evelina) > 8. Re: mri_ca_register from virtual box (Lorenzo Busti) > 9. Re: mri_ca_register from virtual box (Lorenzo Busti) > 10. Converting thickness maps to vtk (Navid Shiee) > 11. Re: tracula and snow leopard: can't allocate region / memory > error (Anastasia Yendiki) > 12. tracula failed to find header file for -t (Scott Hayes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 11 Dec 2011 14:34:05 -0500 > From: Maryam Vaziri Pashkam <mvazir...@gmail.com > <mailto:mvazir...@gmail.com>> > Subject: [Freesurfer] preprocessing error > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <caeexa4cepaydo8epmpma7thadfnd1qcyfg2hnnhz+7svrvb...@mail.gmail.com > > <mailto:caeexa4cepaydo8epmpma7thadfnd1qcyfg2hnnhz%2b7svrvb...@mail.gmail.com>> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am running preprocessing on my data using freesurfer 5.1, fsl > 4.1.7, and > matlab R2009a (I also tried it with matlab 2007a) on Harvard > cluster and I > am receiving an error. I connect to the cluster using terminal and SSH > connection in mac. > > the preprocessing is stalled in the middle with this error: > > ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 > Can't connect? tcp_connect[connect]: Connection timed out > ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz > ** Warning: overwriting file 004/fmcpr.mcdat > Can't connect? tcp_connect[connect]: Connection timed out > Can't connect? tcp_connect[connect]: Connection timed out > Can't connect? tcp_connect[connect]: Connection timed out > > > It does not stop running and output an error. But rather keeps > printing the > last line and does not move forward. Any idea where the problem > might be? > > > Thanks, > Maryam > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111211/c2c91d24/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Sun, 11 Dec 2011 15:39:34 -0500 > From: Douglas Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] preprocessing error > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <4ee51506.6090...@nmr.mgh.harvard.edu > <mailto:4ee51506.6090...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="iso-8859-1" > > what command are you running (I mean the full command line -- hard to > debug without it). The preprocessing should not require matlab. Just > guessing, this does not look like a FS problem. > doug > > On 12/11/11 2:34 PM, Maryam Vaziri Pashkam wrote: > > Hi, > > > > I am running preprocessing on my data using freesurfer 5.1, fsl > 4.1.7, > > and matlab R2009a (I also tried it with matlab 2007a) on Harvard > > cluster and I am receiving an error. I connect to the cluster using > > terminal and SSH connection in mac. > > > > the preprocessing is stalled in the middle with this error: > > > > ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 > > Can't connect? tcp_connect[connect]: Connection timed out > > ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz > > ** Warning: overwriting file 004/fmcpr.mcdat > > Can't connect? tcp_connect[connect]: Connection timed out > > Can't connect? tcp_connect[connect]: Connection timed out > > Can't connect? tcp_connect[connect]: Connection timed out > > > > > > It does not stop running and output an error. But rather keeps > > printing the last line and does not move forward. Any idea where the > > problem might be? > > > > > > Thanks, > > Maryam > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111211/d81510ac/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Mon, 12 Dec 2011 13:24:21 +0800 (CST) > From: Zhangyuanchao <woshizhan...@yahoo.cn > <mailto:woshizhan...@yahoo.cn>> > Subject: [Freesurfer] convert surface label on to functional image > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <1323667461.98732.yahoomailclas...@web92411.mail.cnh.yahoo.com > <mailto:1323667461.98732.yahoomailclas...@web92411.mail.cnh.yahoo.com>> > Content-Type: text/plain; charset="iso-8859-1" > > hi, expert, > By mapping a surface label to a functional template, I want to > extract the corresponding cortical gray matter region in the > functional space. I know I should use the mri_label2vol command.? > In the help page of mri_label2vol, I see some examples of this > command. > 2. Convert a surface label into a binary mask in the functional > space.Fill in all the cortical gray matter. Require that a > functional voxelbe filled at least 30% by the label: > mri_label2vol???--label lh-avg_central_sulcus.label???--temp > f.nii???--reg register.dat???--fillthresh .3???--proj frac 0 1 > .1???--subject bert --hemi lh??--o cent-lh.nii > 3. Convert a surface label into a binary mask in the functional > space.Sample a 1mm ribbon 2mm below the gray/white surface. Do not > require a?fill threshold: > mri_label2vol???--label lh-avg_central_sulcus.label???--temp > f.nii???--reg register.dat???--proj abs -3 -2 .1???--subject bert > --hemi lh??--o cent-lh.nii > I want to extract the cortical gray matter on the functional > images corresponding to the surface label.?I do not know which of > the above commands could obtain the result I want and which > parameters I should use to obtain what I want. > For example 3, I do not quite catch what "Sample a 1mm ribbon 2mm > below the gray/white surface. " this sentence means.? > Thanks for your help! > > Best > Yuanchao > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111212/340b1e36/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Mon, 12 Dec 2011 12:34:05 +0530 > From: Bhavani Shankara Bagepally <bshank...@gmail.com > <mailto:bshank...@gmail.com>> > Subject: [Freesurfer] References/materials for interaction analysis in > freesurfer > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <camx_rar2cqarrgfd5enr4kfiye-+xwnivh-vpktex55zeca...@mail.gmail.com > > <mailto:camx_rar2cqarrgfd5enr4kfiye-%2bxwnivh-vpktex55zeca...@mail.gmail.com>> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Sir/Freesurfer experts, > > We are working of genes and gene- gene interaction on cortical > thickness > using freesurfer. Please let me know if there any > material/publications for > validation of free surfer based analysis mainly on gene-gene > interaction or > any of the Interaction statistics using freesurfer. > > Many thanks in advance > > > -- > Dr. BHAVANI SHANKARA BAGEPALLY > MBBS, (PhD in Clinical Neuroscience) NIMHANS, > Bangalore, > INDIA-560029 > email: bshank...@gmail.com <mailto:bshank...@gmail.com> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111212/00c54edb/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Mon, 12 Dec 2011 18:18:47 +0900 > From: Yuko Yotsumoto <yuk...@a7.keio.jp <mailto:yuk...@a7.keio.jp>> > Subject: Re: [Freesurfer] dt_recon error > To: Douglas Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Cc: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <92101efc-a3b5-4ebc-8b51-3dc392105...@a7.keio.jp > <mailto:92101efc-a3b5-4ebc-8b51-3dc392105...@a7.keio.jp>> > Content-Type: text/plain; charset="us-ascii" > > Thanks Doug, > > In the dt_recon help, > > > The bvalues are in a simple text file, one for each direction > > (including b=0). The bvectors (gradient directions) are also in a > > simple text file with three components on each row. These also > include > > the b=0 values. There must be as many rows in the bvals/bvecs > > as there are frames in the input. > > > I got the bvectors from Siemens tech. The file looks similar to > one in $FREESURFER_HOME/diffusion/mgh-dti-seqpack > > However, I am still not sure about bvalues. > > > The bvalues are in a simple text file, one for each direction > > (including b=0). > > > I think I'm using b-value=700, and I have 64 directions. > Should I have b-values for each of the 64 directions? Then the > text file should have 64 rows and each row has the same value? > > Thank you for your help! > Yuko > > > On Dec 10, 2011, at 1:42 PM, Douglas Greve wrote: > > > Hi Yuko, it will get the bvals and bvecs from a set of tables > > distributed with FS. But the dicom has to have some information > in it > > that tells it which table to use. It looks like your dicom did > not have > > this information (it is not in the info dump created from the > dicom). So > > you'll have to create text files of the bval/bvecs. The expected > format > > is given in the help. You'll have to ask someone who knows about > your > > sequences as to what the actual values you should use. > > doug > > > > On 12/9/11 10:09 PM, Yuko Yotsumoto wrote: > >> Hi Doug, > >> > >> Thank you for your reply. > >>> If so, then it cannot extract the bvecs and bvals. If you > supply them in a file on the command line > >> I don't quite understand how --b works with dt_recon. > >> > >> I did: > >> dt_recon --i > /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm > --s AGY11 --o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > >> > >> and it stopped after creating dwi.nii and dwi-ec.nii. > >> I thought dt_recon is the command to compute bvals and bvecs. > How do I supply bvecs and bvals on the command line? > >> > >> Yuko > >> > >> > >> On Dec 10, 2011, at 2:24 AM, Douglas N Greve wrote: > >> > >>> Hi Yuko, your dicom file might be from a different versioned > scanner than dt_recon is used to seeing. If so, then it cannot > extract the bvecs and bvals. If you supply them in a file on the > command line, it should run properly. > >>> doug > >>> > >>> Yuko Yotsumoto wrote: > >>>> Hello, > >>>> > >>>> I'm having a problem with dt_recon on data scanned by Siemens > TrioTim. > >>>> I'm using v4.5.0, with Mac OS 10.6.8. > >>>> > >>>> dt_recon ran for a while, and stopped with an error "ERROR: > cannot extract sWiPMemBlock.alFree[8] from > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat" > >>>> > >>>> I found the same errors reported to this mailing list, but > found no solution. > >>>> > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html > >>>> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html > >>>> > >>>> In YDTI/YD11A/ folder, I have the following files > >>>> dt_recon.log > >>>> dwi-ec.ecclog > >>>> dwi-ec.nii > >>>> dwi-infodump.dat > >>>> dwi.nii > >>>> mri_glmfit.log > >>>> > >>>> In dwi-infodump.dat, I see bunch of lines, but I don't see > "sWiPMemBlock.alFree". > >>>> > >>>> Please help! > >>>> Thanks, > >>>> Yuko Yotsumoto > >>>> > >>>> > >>>> > >>>> > >>>> #@#------------------------------- > >>>> Fitting Tensors > >>>> Wed Dec 7 10:15:52 JST 2011 > >>>> cd /Users/yuko/Documents/FreeSurfer/subjects > >>>> mri_glmfit --y > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii > --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > --dti > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat > >>>> > >>>> $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > >>>> cwd /Users/yuko/Documents/FreeSurfer/subjects > >>>> cmdline mri_glmfit --y > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii > --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > --dti > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat > sysname Darwin > >>>> hostname Yukos-iMac.local > >>>> machine i386 > >>>> user yuko > >>>> FixVertexAreaFlag = 1 > >>>> UseMaskWithSmoothing 1 > >>>> OneSampleGroupMean 0 > >>>> y > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii > >>>> logyflag 1 > >>>> X > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat > >>>> usedti 1 > >>>> glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > >>>> IllCondOK 0 > >>>> DoFFx 0 > >>>> Creating output directory > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > >>>> Loading y from > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii > >>>> Using DTI > >>>> bValue = 700 > >>>> ERROR: cannot extract sWiPMemBlock.alFree[8] from > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat > >>>> > >>>> > >>>> _______________________________________________ > >>>> 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 <tel:617-724-2358> Fax: > 617-726-7422 <tel:617-726-7422> > >>> > >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>> > >>> > >>> > >>> 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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ----------------------------------- > Yuko Yotsumoto, Ph. D. > Associate Professor (research) > The Global Centers of Excellence Program, Keio University > > TEL:011-81-3-5427-1156 x 23851 <tel:011-81-3-5427-1156%20x%2023851> > e-mail: yuk...@a7.keio.jp <mailto:yuk...@a7.keio.jp> > HP : http://web.keio.jp/~yukoyy/ <http://web.keio.jp/%7Eyukoyy/> > ------------------------------------ > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111212/bf891ff3/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Mon, 12 Dec 2011 19:15:30 +0900 > From: Yuko Yotsumoto <yuk...@a7.keio.jp <mailto:yuk...@a7.keio.jp>> > Subject: Re: [Freesurfer] dt_recon error > To: Douglas Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Cc: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <942cdbdd-4f07-4485-ab91-2a9fbbebd...@a7.keio.jp > <mailto:942cdbdd-4f07-4485-ab91-2a9fbbebd...@a7.keio.jp>> > Content-Type: text/plain; charset="us-ascii" > > Doug, > > Never mind. I think I just figured it out!0 > > Yuko > > On Dec 12, 2011, at 6:18 PM, Yuko Yotsumoto wrote: > > > Thanks Doug, > > > > In the dt_recon help, > > > >> The bvalues are in a simple text file, one for each direction > >> (including b=0). The bvectors (gradient directions) are also in a > >> simple text file with three components on each row. These also > include > >> the b=0 values. There must be as many rows in the bvals/bvecs > >> as there are frames in the input. > > > > > > I got the bvectors from Siemens tech. The file looks similar to > one in $FREESURFER_HOME/diffusion/mgh-dti-seqpack > > > > However, I am still not sure about bvalues. > > > >> The bvalues are in a simple text file, one for each direction > >> (including b=0). > > > > > > I think I'm using b-value=700, and I have 64 directions. > > Should I have b-values for each of the 64 directions? Then the > text file should have 64 rows and each row has the same value? > > > > Thank you for your help! > > Yuko > > > > > > On Dec 10, 2011, at 1:42 PM, Douglas Greve wrote: > > > >> Hi Yuko, it will get the bvals and bvecs from a set of tables > >> distributed with FS. But the dicom has to have some information > in it > >> that tells it which table to use. It looks like your dicom did > not have > >> this information (it is not in the info dump created from the > dicom). So > >> you'll have to create text files of the bval/bvecs. The > expected format > >> is given in the help. You'll have to ask someone who knows > about your > >> sequences as to what the actual values you should use. > >> doug > >> > >> On 12/9/11 10:09 PM, Yuko Yotsumoto wrote: > >>> Hi Doug, > >>> > >>> Thank you for your reply. > >>>> If so, then it cannot extract the bvecs and bvals. If you > supply them in a file on the command line > >>> I don't quite understand how --b works with dt_recon. > >>> > >>> I did: > >>> dt_recon --i > /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm > --s AGY11 --o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > >>> > >>> and it stopped after creating dwi.nii and dwi-ec.nii. > >>> I thought dt_recon is the command to compute bvals and bvecs. > How do I supply bvecs and bvals on the command line? > >>> > >>> Yuko > >>> > >>> > >>> On Dec 10, 2011, at 2:24 AM, Douglas N Greve wrote: > >>> > >>>> Hi Yuko, your dicom file might be from a different versioned > scanner than dt_recon is used to seeing. If so, then it cannot > extract the bvecs and bvals. If you supply them in a file on the > command line, it should run properly. > >>>> doug > >>>> > >>>> Yuko Yotsumoto wrote: > >>>>> Hello, > >>>>> > >>>>> I'm having a problem with dt_recon on data scanned by > Siemens TrioTim. > >>>>> I'm using v4.5.0, with Mac OS 10.6.8. > >>>>> > >>>>> dt_recon ran for a while, and stopped with an error "ERROR: > cannot extract sWiPMemBlock.alFree[8] from > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat" > >>>>> > >>>>> I found the same errors reported to this mailing list, but > found no solution. > >>>>> > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html > >>>>> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html > >>>>> > >>>>> In YDTI/YD11A/ folder, I have the following files > >>>>> dt_recon.log > >>>>> dwi-ec.ecclog > >>>>> dwi-ec.nii > >>>>> dwi-infodump.dat > >>>>> dwi.nii > >>>>> mri_glmfit.log > >>>>> > >>>>> In dwi-infodump.dat, I see bunch of lines, but I don't see > "sWiPMemBlock.alFree". > >>>>> > >>>>> Please help! > >>>>> Thanks, > >>>>> Yuko Yotsumoto > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> #@#------------------------------- > >>>>> Fitting Tensors > >>>>> Wed Dec 7 10:15:52 JST 2011 > >>>>> cd /Users/yuko/Documents/FreeSurfer/subjects > >>>>> mri_glmfit --y > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii > --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > --dti > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat > >>>>> > >>>>> $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > >>>>> cwd /Users/yuko/Documents/FreeSurfer/subjects > >>>>> cmdline mri_glmfit --y > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii > --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > --dti > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat > sysname Darwin > >>>>> hostname Yukos-iMac.local > >>>>> machine i386 > >>>>> user yuko > >>>>> FixVertexAreaFlag = 1 > >>>>> UseMaskWithSmoothing 1 > >>>>> OneSampleGroupMean 0 > >>>>> y > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii > >>>>> logyflag 1 > >>>>> X > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat > >>>>> usedti 1 > >>>>> glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > >>>>> IllCondOK 0 > >>>>> DoFFx 0 > >>>>> Creating output directory > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A > >>>>> Loading y from > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii > >>>>> Using DTI > >>>>> bValue = 700 > >>>>> ERROR: cannot extract sWiPMemBlock.alFree[8] from > /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> 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 <tel:617-724-2358> Fax: > 617-726-7422 <tel:617-726-7422> > >>>> > >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >>>> FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >>>> > >>>> > >>>> > >>>> 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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111212/a92a94db/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Mon, 12 Dec 2011 10:55:05 +0000 > From: Thunell Evelina <evelina.thun...@epfl.ch > <mailto:evelina.thun...@epfl.ch>> > Subject: Re: [Freesurfer] run preproc-sess with -nomc > To: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Cc: "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Message-ID: <33467ed5-576f-4313-8738-332e1fd89...@epfl.ch > <mailto:33467ed5-576f-4313-8738-332e1fd89...@epfl.ch>> > Content-Type: text/plain; charset="us-ascii" > > > Hi Douglas, > > I do most of my analysis in matlab and SPM. For this one part of > my experiment - it's a retinotopic mapping that I will use to > ensure that my ROIs are in V1 - I'm using Freesurfer. I have done > slice time correction, motion correction and coregistration > between functional runs and of the structural image already in > SPM. I thought that since these flags exist they would just skip a > step in the processing and send the data directly to the next > step. But since it's not the case I'll have to do it some other > way instead, maybe just redo the whole preprocessing in Freesurfer > on the already preprocessed data. (Running the analysis with > selxavg3-sess -analysis retlh -s SessXX -no-preproc doesn't work.) > Anyway, the important thing is that the retinotopic mapping data > stay coregistered with the rest of the functional data. If I can > do this step in Freesurfer instead (and the rest of the > preprocessing) that would be an option. > > Thanks a lot, > Evelina > > On Dec 9, 2011, at 7:06 PM, Douglas N Greve wrote: > > Hi Evelina, why do you want to run it without MC? I'm not sure it > will run that way. When you run it with -noreg, it causes it not > to run the registration. For the preprocessing you have set up, it > requires that the registration be run at some point because it > needs it to map the fmri to the surface. > doug > > Thunell Evelina wrote: > > Hi, > > Does anyone know how to correctly use the -nomc and -noreg flags? > > When I run: > preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc > I get the error message: > ERROR: could not determine file for > /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr > > I also tried > preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold > -noreg > which gives the error: > ERROR: cannot find > > /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat > Try running register-sess with -per-run > > When I do > preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold > it works fine and finishes without errors (preproc-sess done) > > (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on > Mac OS X 10.6.8) > > Thanks a lot for any help, > Evelina > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto: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><mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111212/16039e2f/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Mon, 12 Dec 2011 15:41:01 +0100 > From: Lorenzo Busti <lorebu...@gmail.com <mailto:lorebu...@gmail.com>> > Subject: Re: [Freesurfer] mri_ca_register from virtual box > To: Nick Schmansky <ni...@nmr.mgh.harvard.edu > <mailto:ni...@nmr.mgh.harvard.edu>> > Cc: Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <CAKKhoR=p1zsck8vbijzenctotmnx5n5x9fvjetkure6xrwy...@mail.gmail.com > <mailto:p1zsck8vbijzenctotmnx5n5x9fvjetkure6xrwy...@mail.gmail.com>> > Content-Type: text/plain; charset="iso-8859-1" > > *No.. it doesn't work. The RAM is not enough. > > We abandoned that machine.. > > Now we are working with a 64 Bit Computer Dual-core CPU @ 2.10 GHz > with 8 > GB of RAM. > > And.. IT WORKS!!!!! > > We completed the autorecon1, autorecon2 and autorecon3 stages with > succes!! > > We use a virtual box under Windows 7 bat we are not able to > allocate more > than 3.5 GB to run freesurfer. > > At that hight the selecting bar of the virual box is still green (it > becomes red near 4 GB) but passing 3.5 GB the virtual box does not > start > > and it returns the following error > * > > Opening a session for virtual machine frees2 failed. > > VT-x is not available. (VERR_VMX_NO_VMX). > > Unknown error creating VM (VM_VMX_NO_VMX). > > > > Output Code: > > E_FAIL (0x80004005) > > Component: > > Console > > Interface: > > IConsole {515e8e8d-f932-4d8e-9f32-79a52aead882} > > > > > What does it means? > > > Thanks!! > > L. Busti > > > > 2011/12/6 Lorenzo Busti <lorebu...@gmail.com > <mailto:lorebu...@gmail.com>> > > > I'm going to check with more ram dedicated. > > > > Many Thanks > > > > Lorenzo Busti > > > > > > 2011/12/5 Nick Schmansky <ni...@nmr.mgh.harvard.edu > <mailto:ni...@nmr.mgh.harvard.edu>> > > > >> 1.5GB is probably not enough. typically we recommend that > recon-all > >> have at least 3GB available to it, which can be very hard to do > on a > >> virtual machine (since windows takes 1GB, the vm linux takes > another > >> 1GB, which leaves 2GB for processes). i would setup your vm to > use the > >> maximum memory allowed (just dont run stuff in windows at the same > >> time). > >> > >> n. > >> > >> > >> On Mon, 2011-12-05 at 15:01 +0100, Lorenzo Busti wrote: > >> > Hi everyone > >> > I got this error while running one of my subjects > >> > > >> > > >> > mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed > >> > > >> > ERROR: mri_ca_register with non-zero status 252 > >> > > >> > but continuing despite the error > >> > > >> > #-------------------------------------- > >> > > >> > #@# CA Reg Inv Thu Nov 24 05:15:42 EST 2011 > >> > > >> > /home/virtualuser/freesurfer/subjects/Petrollini2/mri > >> > > >> > > >> > > >> > mri_ca_register -invert-and-save transforms/talairach.m3z > >> > > >> > > >> > > >> > Loading, Inverting, Saving, Exiting ... > >> > > >> > Reading transforms/talairach.m3z > >> > > >> > ERROR: cannot find or read transforms/talairach.m3z > >> > > >> > ERROR: mri_ca_register with non-zero status 0 > >> > > >> > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > 01:57:59 > >> > UTC 2009 i686 GNU/Linux > >> > > >> > > >> > > >> > recon-all -s Petrollini2 exited with ERRORS at Thu Nov 24 > 05:15:43 EST > >> > 2011 > >> > > >> > > >> > > >> > To report a problem, > >> > see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > > >> > > >> > I'm working with a virtual machine on a 32 bit computer with > 4GB of > >> > RAM(2-core Intel processor 2.00 GHz). I raised the ram > dedicated to > >> > the virtual machine to 1,5 GB: this is the max value > permitted before > >> > the selecting bar of the virtual box changes from green to > red (is it > >> > sufficent?) > >> > > >> > I have free space for data. > >> > > >> > Can you help me in solving this problem? > >> > > >> > Thanks > >> > > >> > Lorenzo Busti > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > 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 > >> 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. > >> > >> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111212/ae90d1cd/attachment-0001.html > > ------------------------------ > > Message: 9 > Date: Mon, 12 Dec 2011 15:50:37 +0100 > From: Lorenzo Busti <lorebu...@gmail.com <mailto:lorebu...@gmail.com>> > Subject: Re: [Freesurfer] mri_ca_register from virtual box > To: Nick Schmansky <ni...@nmr.mgh.harvard.edu > <mailto:ni...@nmr.mgh.harvard.edu>> > Cc: Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <cakkhorkxidz4l08z+yvffo58ha0_ubu2_ihysmwgsov4cm-...@mail.gmail.com > > <mailto:cakkhorkxidz4l08z%2byvffo58ha0_ubu2_ihysmwgsov4cm-...@mail.gmail.com>> > Content-Type: text/plain; charset="iso-8859-1" > > Ops.. I'm sorry.. > the selecting bar of our virtual box changes from green to red at > 5.4 GB > (not 4 GB.. i was wrong!) > > but if i allocate more than 3.5 GB it does not start! > > Thanks! > > L. Busti > > 2011/12/12 Lorenzo Busti <lorebu...@gmail.com > <mailto:lorebu...@gmail.com>> > > > *No.. it doesn't work. The RAM is not enough. > > > > We abandoned that machine.. > > > > Now we are working with a 64 Bit Computer Dual-core CPU @ 2.10 > GHz with 8 > > GB of RAM. > > > > And.. IT WORKS!!!!! > > > > We completed the autorecon1, autorecon2 and autorecon3 stages with > > succes!! > > > > We use a virtual box under Windows 7 bat we are not able to > allocate more > > than 3.5 GB to run freesurfer. > > > > At that hight the selecting bar of the virual box is still green (it > > becomes red near 4 GB) but passing 3.5 GB the virtual box does > not start > > > > and it returns the following error > > * > > > > Opening a session for virtual machine frees2 failed. > > > > VT-x is not available. (VERR_VMX_NO_VMX). > > > > Unknown error creating VM (VM_VMX_NO_VMX). > > > > > > > > Output Code: > > > > E_FAIL (0x80004005) > > > > Component: > > > > Console > > > > Interface: > > > > IConsole {515e8e8d-f932-4d8e-9f32-79a52aead882} > > > > > > > > > > What does it means? > > > > > > Thanks!! > > > > L. Busti > > > > > > > > > > 2011/12/6 Lorenzo Busti <lorebu...@gmail.com > <mailto:lorebu...@gmail.com>> > > > >> I'm going to check with more ram dedicated. > >> > >> Many Thanks > >> > >> Lorenzo Busti > >> > >> > >> 2011/12/5 Nick Schmansky <ni...@nmr.mgh.harvard.edu > <mailto:ni...@nmr.mgh.harvard.edu>> > >> > >>> 1.5GB is probably not enough. typically we recommend that > recon-all > >>> have at least 3GB available to it, which can be very hard to > do on a > >>> virtual machine (since windows takes 1GB, the vm linux takes > another > >>> 1GB, which leaves 2GB for processes). i would setup your vm > to use the > >>> maximum memory allowed (just dont run stuff in windows at the same > >>> time). > >>> > >>> n. > >>> > >>> > >>> On Mon, 2011-12-05 at 15:01 +0100, Lorenzo Busti wrote: > >>> > Hi everyone > >>> > I got this error while running one of my subjects > >>> > > >>> > > >>> > mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed > >>> > > >>> > ERROR: mri_ca_register with non-zero status 252 > >>> > > >>> > but continuing despite the error > >>> > > >>> > #-------------------------------------- > >>> > > >>> > #@# CA Reg Inv Thu Nov 24 05:15:42 EST 2011 > >>> > > >>> > /home/virtualuser/freesurfer/subjects/Petrollini2/mri > >>> > > >>> > > >>> > > >>> > mri_ca_register -invert-and-save transforms/talairach.m3z > >>> > > >>> > > >>> > > >>> > Loading, Inverting, Saving, Exiting ... > >>> > > >>> > Reading transforms/talairach.m3z > >>> > > >>> > ERROR: cannot find or read transforms/talairach.m3z > >>> > > >>> > ERROR: mri_ca_register with non-zero status 0 > >>> > > >>> > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > 01:57:59 > >>> > UTC 2009 i686 GNU/Linux > >>> > > >>> > > >>> > > >>> > recon-all -s Petrollini2 exited with ERRORS at Thu Nov 24 > 05:15:43 EST > >>> > 2011 > >>> > > >>> > > >>> > > >>> > To report a problem, > >>> > see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>> > > >>> > > >>> > I'm working with a virtual machine on a 32 bit computer with > 4GB of > >>> > RAM(2-core Intel processor 2.00 GHz). I raised the ram > dedicated to > >>> > the virtual machine to 1,5 GB: this is the max value > permitted before > >>> > the selecting bar of the virtual box changes from green to > red (is it > >>> > sufficent?) > >>> > > >>> > I have free space for data. > >>> > > >>> > Can you help me in solving this problem? > >>> > > >>> > Thanks > >>> > > >>> > Lorenzo Busti > >>> > > >>> > > >>> > > >>> > > >>> > _______________________________________________ > >>> > 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 > >>> 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. > >>> > >>> > >> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111212/c0b5ba14/attachment-0001.html > > ------------------------------ > > Message: 10 > Date: Mon, 12 Dec 2011 10:13:01 -0500 > From: Navid Shiee <na...@jhu.edu <mailto:na...@jhu.edu>> > Subject: [Freesurfer] Converting thickness maps to vtk > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <CAMn7hwjTsYQ4EiUevNeSbKNKAUwg8gfYQ=tpbhwtx7p8v8c...@mail.gmail.com > <mailto:tpbhwtx7p8v8c...@mail.gmail.com>> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I was wondering if there is a command like mris_convert to create a > thickness map in vtk format (either on the white or pial surface) ? > > Thanks, > > -- > Navid Shiee > Ph.D. Candidate > Laboratory of MEDical Image Computing (MEDIC) > Image Analysis and Communication Laboratory (IACL) > Johns Hopkins University > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20111212/b483aee1/attachment-0001.html > > ------------------------------ > > Message: 11 > Date: Mon, 12 Dec 2011 10:20:59 -0500 (EST) > From: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu > <mailto:ayend...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] tracula and snow leopard: can't allocate > region / memory error > To: Scott Hayes <smha...@bu.edu <mailto:smha...@bu.edu>> > Cc: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <alpine.lrh.2.00.1112121017410.7...@door.nmr.mgh.harvard.edu > <mailto:alpine.lrh.2.00.1112121017410.7...@door.nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Scott - Sending to the list is always good so that others can > find it > in the archives when they have similar problems. > > Do you specify the .dcm or .mgz file in your dmrirc? Does > dwi.nii.gz have > the right dimensions/frames? > > a.y > > On Mon, 12 Dec 2011, Scott Hayes wrote: > > > Thanks for the prompt response Anastasia--I ran it over the weekend > > and it worked. > > > > I've subsequently encountered a new issue (copied below from the > > trac-all.log). The file (dwi.nii.gz) exists in the correct location > > (it was written there by tracula). I use unpacksdcmdir for > unpacking > > the dicoms, and then point the config file to the appropriate .mgz > > file, so I'm not doing anything particularly unusual in terms of > > unpacking or messing w/ the headers (We scan on a Siemens 3T tim > > trio.) I can send this to the listserv if you prefer. > > Best, > > Scott > > > > fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k > > > > /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz > > -m -s | awk '{print $1/$2}' > > > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt > > ** ERROR (nifti_image_read): failed to find header file for '-t' > > ** ERROR: nifti_image_open(-t): bad header info > > Error: failed to open file -t > > ERROR: Could not open image -t > > Image Exception : #22 :: Failed to read volume -t > > terminate called after throwing an instance of > 'RBD_COMMON::BaseException' > > > > > > > > On Fri, Dec 9, 2011 at 12:44 PM, Anastasia Yendiki > > <ayend...@nmr.mgh.harvard.edu > <mailto:ayend...@nmr.mgh.harvard.edu>> wrote: > >> > >> Hi Scott - Here are the tracula executables for snow leopard > that we posted > >> in response to that thread: > >> > >> > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz > >> > >> Let me know if this solves the memory errors. > >> > >> a.y > >> > >> > >> On Fri, 9 Dec 2011, Scott Hayes wrote: > >> > >>> Hi Anastasia, > >>> I've encountered an error using tracula w/ snow leopard OS > that was > >>> previously reported on the FS listserv: > >>> > >>> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18829.html > >>> > >>> I'm wondering if there is a documented solution available? > >>> Recompiling from source code would be beyond my expertise. > >>> > >>> David: ?I'm cc'ing you just as a heads up--all of the > workstations in > >>> the imaging center run snow leopard OS. > >>> > >>> Best, > >>> Scott > >>> > >> > >> > >> 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. > >> > > > > > > > > > > ------------------------------ > > Message: 12 > Date: Mon, 12 Dec 2011 11:31:57 -0500 > From: Scott Hayes <smha...@bu.edu <mailto:smha...@bu.edu>> > Subject: [Freesurfer] tracula failed to find header file for -t > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <caf9yudz+psciq-axs5l2m6tg3e5qsrn0jyc9qr9kmjxg+py...@mail.gmail.com > > <mailto:caf9yudz%2bpsciq-axs5l2m6tg3e5qsrn0jyc9qr9kmjxg%2bpy...@mail.gmail.com>> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > I have received the following error message (copied from > trac-all.log file). > > fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k > > /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz > -m -s | awk '{print $1/$2}' > > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt > ** ERROR (nifti_image_read): failed to find header file for '-t' > ** ERROR: nifti_image_open(-t): bad header info > Error: failed to open file -t > ERROR: Could not open image -t > Image Exception : #22 :: Failed to read volume -t > terminate called after throwing an instance of > 'RBD_COMMON::BaseException' > > > The file (dwi.nii.gz) exists in the correct location, and appears to > have the correct number of frames (60 directions + 10 b0). > We scan on a Siemens 3T tim trio. I unpack the data using > unpacksdcmdir and I specify the resulting .mgz file in the tracula > config file. Running locally on mac os 10.6.8. > > Any suggestions would be appreciated. > Thanks, > Scott > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 94, Issue 13 > ****************************************** > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
