So the dicom did not come from the scanner? You can use that nifti file as input instead, but you should view it in freeview to make sure it is oriented correctly
On 04/05/2018 03:46 PM, Kan Ding wrote: > The data has been analyzed. The scan information from corresponding NIFTI > file as following: > > nua502608:3T8619 kding$ mri_info 3T8619_T1.nii.gz > Volume information for 3T8619_T1.nii.gz > type: nii > dimensions: 160 x 256 x 256 > voxel sizes: 1.000000, 1.000000, 1.000000 > type: FLOAT (3) > fov: 160.000 > dof: 0 > xstart: -80.0, xend: 80.0 > ystart: -128.0, yend: 128.0 > zstart: -128.0, zend: 128.0 > TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees > nframes: 1 > PhEncDir: UNKNOWN > FieldStrength: 0.000000 > ras xform present > xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = > 0.0107 > : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = > 7.8592 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = > -15.4014 > Orientation : LPS > Primary Slice Direction: axial > > voxel to ras transform: > -1.0000 -0.0000 -0.0000 80.0107 > -0.0000 -1.0000 -0.0000 135.8592 > 0.0000 0.0000 1.0000 -143.4014 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant 1 > > ras to voxel transform: > -1.0000 0.0000 0.0000 80.0107 > 0.0000 -1.0000 0.0000 135.8592 > 0.0000 0.0000 1.0000 143.4014 > 0.0000 0.0000 0.0000 1.0000 > > > > > > Date: Thu, 5 Apr 2018 12:59:16 -0400 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] scan log generated by dcmunpack > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <22ecfa88-e463-169b-03c5-4c25ac224...@mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252"; format=flowed > > It looks like there is something wrong with that dicom file/series > because the pixel spacing is "unknown". Where did the dicoms from from? > Have they been anonymized? > > > On 04/05/2018 12:12 PM, Kan Ding wrote: >> Hello: >> >> I am trying to unpack my DICOM folder and run recon-all. After >> dcmunpack, I selected 301 to run recon-all. But the recon-all didn?t >> go through. Please see the attached scan.log, recon-all.log, >> error.log, and the pic of my DICOM folder. >> >> Thank you so mch. >> >> Kan Ding, MD >> > > > On 4/5/18, 3:21 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu" > <reesurfer-boun...@nmr.mgh.harvard.edu on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.nmr.mgh.harvard.edu/mailman/istinfo/freesurfer >> or, via email, send a message with subject or body 'help' to >> freesurfer-requ...@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> 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. scan log generated by dcmunpack (Kan Ding) >> 2. Re: recon-all: exited with errors (white matter peak at 110, >> cannot allocate memory) (Bruce Fischl) >> 3. Re: recon-all: exited with errors (white matter peak at 110, >> cannot allocate memory) (srishti goel) >> 4. Qdec+Table format issue ????? (Dimitrios Trifonopoulos) >> 5. Re: recon-all: exited with errors (white matter peak at 110, >> cannot allocate memory) (Bruce Fischl) >> 6. Re: recon-all: exited with errors (whit matter peak at 110, >> cannot allocate memory) (srishti goel) >> 7. Re: recon-all: exited with errors (white matter peak at 110, >> cannot allocate memory) (Bruce Fischl) >> 8. Re: recon-all: exited with errors (white matter peak at 110, >> cannot allocate memory) (srishti goel) >> 9. Re: recon-all: exited with errors (white matterpeak at 110, >> cannot allocate memory) (Bruce Fischl) >> 10. Re: recon-all: exited with errors (white matter peak at 110, >> cannot allocate memory) (srishti goel) >> 11. Re: recon-all: exited with errors (white matter peak at 110, >> cannot allocate memory) (Bruce Fischl) >> 12. Re: mri_vol2surf: unable to compare volume maps (Douglas N. Greve) >> 13. Re: scan log generated by dcmunpack (Douglas N. Greve) >> 14. Time Series to Surface (Crawford, Anna) >> 15. Tracula - Could not find satisfactory control point fit >> (Lussier,Desiree) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 5 Ap 2018 16:12:43 +0000 >> From: Kan Ding <kan.d...@utsouthwestern.edu> >> Subject: [Freesurfer] scan log generated by dcmunpack >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <d6ebc339.10ff3%kan.d...@utsouthwestern.edu> >> Contnt-Type: text/plain; charset="iso-8859-1" >> >> Hello: >> >> I am trying to unpack my DICOM folder and run recon-all. After dcmunpack, >> I selected 301 to run recon-all. But the recon-all didn't go through. >> Please see the attached scan.log, recon-all.log, error.log, and the pic >> of my DICOM folder. >> >> Thank you so much. >> Kan Din, MD >> Assistant Professor- Department of Neurology and Neurotherapeutics >> UT Southwestern Medical Center at Dallas >> Tel: 214-648-9197 >> Fax: 214-648-6320 >> >> ________________________________ >> >> UT Southwestern >> >> >> Medical Center >> >> >> >> The future of medicine, today. >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> ecf515aa/attachment-0001.html >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: scan.log >> Type: application/octet-stream >> Size: 1162 bytes >> Desc: scan.log >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> ecf515aa/attachment-0003.obj >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: recon-all.log >> Type: application/octet-stream >> Size: 25046 bytes >> Desc: recon-all.log >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> ecf515aa/attachment-0004.obj >> ------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: Screen Shot 2018-04-05 at 11.14.54 AM.png >> Type: image/png >> Size: 110734 bytes >> Desc: Screen Shot 2018-04-05 at 11.14.54 AM.png >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> ecf515aa/attachmet-0001.png >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: error.log >> Type: application/octet-stream >> Size: 62 bytes >> Desc: error.log >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> ecf515aa/attachment-0005.obj >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 5 Apr 2018 12:16:26 -0400 (EDT) >> From: Bruce Fischl <fi...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfersupport list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <alpine.lrh.2.21.1804051215360.18...@tiamat.nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Srishti >> >> are you sure that your machine didn't just run out of memory? The >> recon-all.log file includes the amount of free (and total) memory at the >> timethe process was started. >> >> cheers >> Bruce >> >> On Thu, 5 Apr >> 2018, srishti goel wrote: >> >>> Hi, >>> I have been trying to edit structural brains and very few times I wuld >>> get the following error while running recon-all -s >>> subjID >>> >>> white matter peak fond at 110 >>> cannot allocate memory >>> >>> Upon looking at the archive, tere was only one similar issue and it >>> was recommend to check mri_info as the brain mask might >>> have been corrupted. I did that and here is the output: >>> >>> olume information for brainmask.mgz >>> >>> ? ? ? ? ? type: MGH >>> >>> ? ? dimensions: 256 x 256 x 256 >>> >>> ?? voxel sizes: 1.000000, 1.000000, 1.000000 >>> >>> ? ? ? ? ? type: UCHAR (0) >>> >>> ?? ? ? ? ? fov: 256.000 >>> >>> ?? ? ? ? ? dof: 0 >>> >>> ? ? ? ? xstart: -128.0, xend: 128.0 >>> >>> ? ? ? ? ystart: -128.0, yend: 128.0 >>> >>> ? ? ? ? zstart: -128.0, zend: 128.0 >>> >>> ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: >>> 0.00 degrees >>> >>> ?? ? ? nframes: 1 >>> >>> ?? ? ? PhEncDir: UNKNOWN >>> >>> ?? ? ? FieldStrength: 0.000000 >>> >>> ras xform present >>> >>> ? ? xform info: x_r =? -1.0000, y_r = ? 0.0000, z_r = ? .0000, c_r =? >>> ? -1.0000 >>> >>> ? ? ? ? ? ? ? : x_a = ? 0.0000, y_a = ? 0.0000, z_a = ? 1.0000, c_a =? >>> ? 37.500 >>> >>> ? ? ? ? ? ? ? : x_s = ? 0.0000, y_s =? -1.0000, z_s = ? 0.0000, c_s = ? >>> ? 4.7185 >>> >>> >>> talairach xfm : >>> /pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/tala >>> irach.xfm >>> >>> Orientation ? : LIA >>> >>> Primary Slice Direction: coronal >>> >>> >>> voxel to ras transform: >>> >>> ?? ? ? ? ? ? ? -1.0000 ? 0.0000 ? 0.0000? 127.0000 >>> >>> ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 1.0000 ? -90.5000 >>> >>> ? ? ? ? ? ? ? ? 0.0000? -1.0000 ? 0.0000 ? 132.7185 >>> >>> ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 0.0000 ? 1.0000 >>> >>> >>> voxel-to-ras determinant -1 >>> >>> >>> ras to voxel transform: >>> >>> ?? ? ? ? ? ? ? -1.0000? -0.0000? -0.0000 ? 127.0000 >>> >>> ?? ? ? ? ? ? ? -0.0000? -0.0000? -1.000 ? 132.7185 >>> >>> ?? ? ? ? ? ? ? -0.0000 ? 1.0000? -0.0000? ? 90.5000 >>> >>> ?? ? ? ? ? ? ? -0.0000? -0.0000? -0.0000 ? ? 1.0000 >>> >>> >>> Is there any other ay to resolve this issue than reconstruction the >>> brain again and doing all the edits all over again hoping >>> that the?brain mask does not get corrupted this time? >>> >>> Appreciate any help with this. >>> >>> Best, >>> Srishti >>> >>> >> ------------------------------ >> > Message: 3 >> Date: Thu, 5 Apr 2018 12:19:06 -0400 >> From: srishti goel <23srishtigoel@gmailcom> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <CAGqM=zimvc9-jevnkodro2jeo8nwmbytmxbbd4qexnkedu...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Bruce, >> >> The machine definitely hasn't run out of memory. Here is the memory usage > >from recon-all.log >> total used free >> shared buff/cache available >> Mem: 263726968 34330048 152102696 12944 77294224 >> 191963372 >> Swap: 2097148 0 2097148 >> >> >> >> >> Best, >> Srishti >> Soial/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 218 at 12:16 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> >>> Hi Srishti >>> >>> are you sure that your machine didn't just run out of memry? The >>> recon-all.log file includes the amount of free (and total) memory at the >>> time the processwas started. >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> Hi, >>>> I have been trying to edit structural brains and very few times I would >>>> get the following error while running recon-all -s >>>> subjID >>>>>>> white matter peak found at 110 >>>> cannot allocate memory >>>> >>>> Upon looking at the archive, there was only one similar issue and it >>>> was >>>> recommed to check mri_info as the brain mask might >>>> have been corrupted. I did that and here is the output >>>> >>>> Volume information for brainmask.mgz >>>> >>>> type: MGH >>>> >>>> dimensions: 256 x 256 x 256 >>>> >>>> voxel sizes: 1.000000, 1.000000, 1.000000 >>>> >>>> type: UCHAR (0) >>>> >>>> fov: 256.000 >>>> >>>> dof: 0 >>>> >>>> xstart: -128.0, xend: 128.0 >>>> >>>> ystart: -128.0, yend: 128.0 >>>> zstart: -128.0, zend: 128.0 >>>> >>>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: >>>> 0.00 >>>> degrees >>>> >>>> nframes: 1 >>>> PhEncDir: UNKNOWN >>>> >>>> FieldStrength: 0.000000 >>>> >>>> rasxform present >>>> >>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = >>>> -1.0000 >>>>>>> : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = >>>> 37.5000 >>>> >>>> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = >>>> 4.7185 >>>> >>>> >>>> talairach xfm : /pine/scr/s/r/srishtig/Duke_Te >>> st/Freesurfer_out/11039/mri/transforms/talairach.xfm >>>> Orientation : LIA >>>> >>>> rimary Slice Direction: coronal >>>> >>>> >>>> voxel to ras transform: >>>> >>>> -.0000 0.0000 0.0000 127.0000 >>>> >>>> 0.0000 0.0000 1.0000 -905000 >>>> >>>> 0.0000 -1.0000 0.0000 132.7185 >>>> >>>> 0.0000 0.0000 0.0000 1.0000 >>>> >>>> >>>> voxel-to-ras determinant -1 >>>> >>>> >>>> ras to voxel transform: >>>> >>>> -1.0000 -0.0000 -0.0000 127.0000 >>>> >>>> -0.0000 -0.0000 -1.0000 132.7185 >>>> >>>> 0.0000 1.0000 -0.0000 90.5000 >>>> >>>> -0.0000 -0.0000 -0.0000 1.0000 >>>> >>>> >>>> Is there any other way to resolve this issue than reonstruction the >>>> brain again and doing all the edits all over again hoping >>>> that the brain mask des not get corrupted this time? >>>> >>>> Appreciate any help with this. >>>> >>>> Best, >>>> Srishti >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> freesr...@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, pleae 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/20180405/ >> 8339745b/attachment-0001.html >> >> ----------------------------- >> >> Message: 4 >> Date: Thu, 5 Apr 2018 16:12:26 +0000 >> From: Dimitrios Trifonopoulos <trif...@otmail.com> >> Subject: [Freesurfer] Qdec+Table format issue ????? >> To: "freesurfer@nmr.mgh.harvard.edu" <freesr...@nmr.mgh.harvard.edu> >> Message-ID: >> <AM5PR0701MB2291CD465CB533E255D8BFDF90BB0@AM5PR0701MB2291.eurprd07prod.o >> utlook.com> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear Recipient, >> >> >> I am a aster student new comer in FS. I am trying toi use the QDEC ti >> analyse some longitudinal data. Most probably my issue is related with >> the file format. I tried to use several txt editors (mac text editor, >> gedit and text wrangler) however I end up in 2 different errors without >> be abe to overcome the issue. >> >> The 1st error was: >> >> >> ERROR: qdec table missing correct column headers? >> >> Make sure first column is labeled 'fsid' for the time point and >> >> second column is 'fsid-base' t specify the subject tempate >> (base), e.g.: >> >> >> fsid fsid-base age >> >> me1 me 22.3 >> >> me2 me 23.2 >> >> you1 you 21.6 >> >> you2 you 22.5 >> >> >> Simones-iMac:subects SLMAC14$ long_mris_slopes --qdec >> /Applications/freesurfer/subjects/qdec/lala copy.dat.doc --meas tickness >> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label >> -time years --qcache fsaverage --sd /Applications/freesurfer/subjects/ >> >> >> and the 2nd one was: >> >> >> Parsing the qdec table: >> /Applications/freesurfer/subjects/qec/qdec.table.dat >> >> ERROR: qdec table /Applications/freesurfer/subjects/qdec/qdec.table.dat >> not found or empty? >> >> >> Even if I found a similar error im the forum, I didn't undestand finally >> how this guy overcome it. I also attached you the 2 files that I used. >> Please answer me as soon as you are available. Thank you >> >> >> All the Best, >> >> Dimitris >> >> >> >> >> >> >> -------------- next part ------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 3463af2e/attachmen-0001.html >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: qdec.table.dat >> Type: application/octet-stream >> Size: 1339 bytes >> Desc: qdec.table.dat >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 3463af2e/attachment-0001.obj >> ------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: lala copy.dat.rtf >> Type: text/rtf >> Size: 646 bytes >> Desc:lala copy.dat.rtf >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 3463af2e/attachment-0001.rtf >> >> ------------------------------ >> >> Message: 5 >> Date: Th, 5 Apr 2018 12:24:42 -0400 (EDT) >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <alpine.lrh.2.20.1804051224100.9...@gate.nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> if ou run the command that failed again on the command line directly >> (that >> is, not in recon-all) does it fail again? >> >> On Thu, 5 Apr 2018, srishi goel wrote: >> >>> Hi Bruce, >>> >>> The machine definitely hasn't run out of memory. Here is the memory >> usage >>> from recon-all.log ? >>> >>> ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ? ? ?used ? ? ? ?free ? ? ? ? ? ?? >>> ? ? >>> shared ?buff/cache ? available >>> Mem: ? ? ?263726968 ? ?34330048 ? 152102696 ? ? ? 12944 ? ?77294224 >>> 191963372 >>> Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ? ? ? ? ? 2097148 >>> >>> >>> >>> >>> Best, >>> Srisht >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Srishti >>> >>> are you sure that your machine didn't just run out of memory? >>> The recn-all.log file includes the amount of free (and total) >>> memory at the time the process as started. >>> >>> cheers >>> Bruce >>> >>> ?On Thu, 5 Apr 2018, srishti goel wrot: >>> >>> Hi, >>> I have been trying to edit structural brains and >>> very few times I would get the following error while >>> running recon-all -s >>> subjID >>> >>> white matter peak found at 110 >>> cannot allocate memory >>> >>> Upon looking at the archive, there was only one >>> similar issue and it was recommend to check mri_info >>> as the brain mask might >>> have been corrupted. I did that and here is te >>> output: >>> >>> Volume information for brainmask.mgz >>>>> ? ? ? ? ? type: MGH >>> ? ? dimensions: 256 x 256 x 56 >>> >>> ?? voxel sizes: 1.000000, 1.000000, 1.000000 >>> >>> ? ? ? ? type: UCHAR (0) >>> >>> ?? ? ? ? ? fov: 256.000 >>> >>> ?? ? ? ? dof: 0 >>> >>> ? ? ? ? xstart: -128.0, xend: 128.0 >>> >>> ? ? ? ? ystart: -128.0, yend: 128.0 >>> >>> ? ? ? ? zstart: -128.0, zend: 128.0 >>> >>> ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 >>> msec, flip angle: 0.00 degrees >>> >>> ?? ? ? nframes: 1 >>> >>> ?? ? ? PhEncDir: UNKNOWN >>> >>> ?? ? ? FieldStrength: 0.000000 >>> >>> ras xform present >>> >>> ? ? xform info: x_r =? -1.0000 y_r = ? 0.0000, z_r >>> = ? 0.0000, c_r =? ? -1.0000 >>> >>> ? ? ? ? ? ? ? : x_a = ? 0.000, y_a = ? 0.0000, z_a >>> = ? 1.0000, c_a =? ? 37.5000 >>> >>> ? ? ? ? ? ? ? : x_s = ? 0.0000, y_s =? -1.0000, z_s >>> = ? 0.0000, c_s = ? ? 4.7185 >>> >>> >>> alairach xfm >>> :/pine/scr/s/r/srishtig/Duke_Test/Freesurfr_out/11039/mri/transforms/tal >>> air >>> ach.xfm >>> >>> Orientation ? : LIA >>> >>> Primary Slice Direction: coronal >>> >>> >>> voxel to ras transform: >>> >>> ?? ? ? ? ? ? ? -1.0000 ? 0.0000 ? 0.0000 ? 127.0000 >>> >>> ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 1.0000 ? -9.5000 >>> >>> ? ? ? ? ? ? ? ? 0.0000? -1.0000 ? 0.0000 ? 132.7185 >>> >>> ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 00000 ? ? 1.0000 >>> >>> >>> voxel-to-ras determinant -1 >>> >>> >>> ras to voxel transform: >>> >>> ?? ? ? ? ? ? -1.0000? -0.0000? -0.0000 ? 127.0000 >>> >>> ?? ? ? ? ? ? ? 0.0000? -0.0000? -1.0000 ? 132.7185 >>> >>> ?? ? ? ? ? ? -0.0000 ? 1.0000? -0.0000? ? 90.5000 >>> >>> ?? ? ? ? ? ? ? -0.0000? -0.0000? -0.0000 ? ? 1.0000 >>> >>> >>> Is there any other way to resolve this issue than >>> reconstruction the brain again and doing all the >>> edits all over again hoping >>> that the?brain mask does not get corrupted this >>> time? >>> >>> Appreciate any help with this. >>> >>> Best, >>> Srishti >>> >>> >>> _______________________________________________ >>> 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-mai was sent to you in error and the >>> e-mail >>> contains patient informatin, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but dos not contain patient information, please contact the sender >>> and proprly >>> dispose of the e-mail. >>> >>> >>> >>> >> ----------------------------- >> >> Message: 6 >> Date: Thu, 5 Apr 2018 12:29:48 -0400 >> From: srishti goel <23srishtig...@gmail.com> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <CAGqM=zgn1hmae0_nzurz1p-t3jr2syx-j1v4+hzoetz_nx9...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> I am sorry, I am not sure what do you mean by running the command line >> directly? >> >> I use the following command: >> >> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user >> srish...@email.unc.edu --wrap "export >> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >> recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa" >> >> >> where sbatch..... until export is our local server submission command and >> I >> run this command from the command line itself, not using any script. >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Caolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.gel12 >> >> >> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fis...@nmr.mgh.harard.edu> >> wrote: >> >>> if you run the command that failed again on the cmmand line directly >>> (that is, not in recon-all) does it fail again? >>> >>> >>> On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> Hi Bruce, >>>> The machine definitely hasn't run out of memory. Here is the memory >>>> usage >>>> from recon-all.log >>>> >>>> total used free >>>> shared buff/cache available >>>> Mem: 263726968 34330048 152102696 12944 77294224 >>>> 191963372 >>>> Swap: 2097148 0 207148 >>>> >>>> >>>> >>>> >>>> Best, >>>> Srishti >>>> Social/Clinical ResearchSpecialist >>>> Child Imaging Research and Life Experiences Lab >>>> Univrsity of North Carolina at Chapel Hill >>>> email (W): srish...@email.unc.ed >>>> skype: srishti.goel12 >>>> >>>> >>>> On Thu, Apr 5, 2018 at 12:16 PM, ruce Fischl >>>> <fis...@nmr.mgh.harvard.edu >>>> wrote: >>>> Hi rishti >>>> >>>> are you sure that your machine didn't just run out ofmemory? >>>> The recon-all.log file includes the amount of free (nd total) >>>> memory at the time the process was started. >>>> >>>> cheers >>>> Bruce >>>> >>>> On Thu, 5 Apr 2018, srishti goel wrote: >>>> >>>> Hi, >>>> I have been trying to edit structural brains and >>>> very few times I would get the following error whie >>>> running recon-all -s >>>> subjID >>>> >>>> white matter peak found at 110 >>>> cannot allocate memory >>>> >>>> Upon looking at the archive, there was only one >>>> similar issue and it was recommend to check mri_info >>>> as the brain mask might >>>> have been corrupted. I did that and here is the >>>> output: >>>> >>>> Volume information for brainmask.mgz >>>> >>>> type: MGH >>>> >>>> dimensins: 256 x 256 x 256 >>>> >>>> voxel sizes: 1.000000, 1.00000, 1.000000 >>>> >>>> type: UCHAR (0) >>>> >>>> fov: 256.000 >>>> >>>> dof: 0 >>>> >>>> xstart: -128.0, xend: 128.0 >>>> >>>> ystart: -128.0, yend: 128.0 >>>> >>>> zstart: -128.0, zend: 128.0 >>>> >>>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 >>>> msec, flip angle:0.00 degrees >>>> >>>> nframes: 1 >>>> >>>> PhEncDir: UNKNOWN >>>> >>>> FieldStrength: 0.000000 >>>> >>>> ras xform present >>>> >>>> xform info: x_r = -1.0000, y_r = 0.0000, z_r >>>> = 0.0000, c_r = -1.0000 >>>> >>>> : x_a = 0.0000, y_a = 0.0000, z_a >>>> = .0000, c_a = 37.5000 >>>> >>>> : x_s = 0.0000, y_s = -1.0000, z_s >>>> = 0.0000, c_s = 4.7185 >>>> >>>> >>>> talairach xfm :/pine/scr/s/r/srishtig/Duke_T >>>> est/Freesurfer_out/11039/mri/transforms/talair >>>> ach.xfm >>>> >>>> Orientation : LIA >>>> >>>> Primary Slice Direction: coronal >>>> >>>> >>>> voxel to ras transform: >>>> >>>> -1.0000 0.0000 0.0000 127.0000 >>>> >>>> 0.0000 0.0000 1.0000 -90.5000 >>>> >>>> 0.0000 -1.0000 0.0000 132.7185 >>>> >>>> 0.0000 0.0000 0.0000 1.0000 >>>> >>>> >>>> voxel-to-ras determinant -1 >>>> >>>> >>>> ras to voxel transform: >>>> >>>> -1.0000 -0.0000 -0.0000 127.0000 >>>> >>>> -0.0000 -0.0000 -1.0000 132.7185 >>>> >>>> -0.0000 1.0000 -0.0000 90.5000 >>>> >>>> -0.0000 -0.0000 -0.0000 1.0000 >>>> >>>> >>>> Is there any other way to resolve this issue than >>>> reconstruction the brain again and doing all the >>>> edits all over again hoping >>>> that the brain mask does not get corrupted this >>>> time? >>>> >>>> Appreciate any help with this. >>>> >>>> Best, >>>> Srishti >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 31b09f2c/attachment-0001.html >> >> ------------------------------ >> >> Message: 7 >> Date: Thu, 5 Apr 2018 12:31:43 -0400 (EDT) >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <alpine.lrh.2.21.1804051231080.18...@tiamat.nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Srishti >> >> if you look in the subject's scripts dir there should be a file named >> "recon-all.cmd". Try rerunning the last command in it (probably from the >> mri dir) >> >> cheers >> Bruce >> On Thu, 5 Apr 2018, srishti goel wrote: >> >>> I am sorry, I am not sure what do you mean by running the command line >>> directly? >>> I use the following command: >>> >>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user >>> srish...@email.unc.edu --wrap "export >>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >>> recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa" >>> >>> >>> where sbatch..... until export is our local server submission command >>> and I run this command from the command line itself, not >>> using any script. >>> >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> if you run the command that failed again on the command line >>> directly (that is, not in recon-all) does it fail >>> again? >>> >>> On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> Hi Bruce, >>> >>> The machine definitely hasn't run out of memory. Here is >>> the memory usage >>> from recon-all.log ? >>> >>> ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ? ? ?used ? ? ? ?free ? >>> ? ? ? ? ? ? ? ? >>> shared ?buff/cache ? available >>> Mem: ? ? ?263726968 ? ?34330048 ? 152102696 ? ? ? 12944 ? >>> ?77294224 ? >>> 191963372 >>> Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ? ? ? ? ? 2097148 >>> >>> >>> >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> >>> wrote: >>> ? ? ? Hi Srishti >>> >>> ? ? ? are you sure that your machine didn't just run out of >>> memory? >>> ? ? ? The recon-all.log file includes the amount of free >>> (and total) >>> ? ? ? memory at the time the process was started. >>> >>> ? ? ? cheers >>> ? ? ? Bruce >>> >>> ? ? ? ?On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> ? ? ? ? ? ? Hi, >>> ? ? ? ? ? ? I have been trying to edit structural brains and >>> ? ? ? ? ? ? very few times I would get the following error >>> while >>> ? ? ? ? ? ? running recon-all -s >>> ? ? ? ? ? ? subjID >>> >>> ? ? ? ? ? ? white matter peak found at 110 >>> ? ? ? ? ? ? cannot allocate memory >>> >>> ? ? ? ? ? ? Upon looking at the archive, there was only one >>> ? ? ? ? ? ? similar issue and it was recommend to check >>> mri_info >>> ? ? ? ? ? ? as the brain mask might >>> ? ? ? ? ? ? have been corrupted. I did that and here is the >>> ? ? ? ? ? ? output: >>> >>> ? ? ? ? ? ? Volume information for brainmask.mgz >>> >>> ? ? ? ? ? ? ? ? ? ? ? type: MGH >>> >>> ? ? ? ? ? ? ? ? dimensions: 256 x 256 x 256 >>> >>> ? ? ? ? ? ? ?? voxel sizes: 1.000000, 1.000000, 1.000000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? type: UCHAR (0) >>> >>> ? ? ? ? ? ? ?? ? ? ? ? fov: 256.000 >>> >>> ? ? ? ? ? ? ?? ? ? ? ? dof: 0 >>> >>> ? ? ? ? ? ? ? ? ? ? xstart: -128.0, xend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? ystart: -128.0, yend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? zstart: -128.0, zend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00 msec, TI: >>> 0.00 >>> ? ? ? ? ? ? msec, flip angle: 0.00 degrees >>> >>> ? ? ? ? ? ? ?? ? ? nframes: 1 >>> >>> ? ? ? ? ? ? ?? ? ? PhEncDir: UNKNOWN >>> >>> ? ? ? ? ? ? ?? ? ? FieldStrength: 0.000000 >>> >>> ? ? ? ? ? ? ras xform present >>> >>> ? ? ? ? ? ? ? ? xform info: x_r =? -1.0000, y_r = ? 0.0000, >>> z_r >>> ? ? ? ? ? ? = ? 0.0000, c_r =? ? -1.0000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? : x_a = ? 0.0000, y_a = ? 0.0000, >>> z_a >>> ? ? ? ? ? ? = ? 1.0000, c_a =? ? 37.5000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? : x_s = ? 0.0000, y_s =? -1.0000, >>> z_s >>> ? ? ? ? ? ? = ? 0.0000, c_s = ? ? 4.7185 >>> >>> >>> ? ? ? ? ? ? talairach xfm >>> :/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/tal >>> air >>> ? ? ? ? ? ? ach.xfm >>> >>> ? ? ? ? ? ? Orientation ? : LIA >>> >>> ? ? ? ? ? ? Primary Slice Direction: coronal >>> >>> >>> ? ? ? ? ? ? voxel to ras transform: >>> >>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000 ? 0.0000 ? 0.0000 ? >>> 127.0000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 1.0000 ? >>> -90.5000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000? -1.0000 ? 0.0000 ? >>> 132.7185 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? 0.0000 ? ? >>> 1.0000 >>> >>> >>> ? ? ? ? ? ? voxel-to-ras determinant -1 >>> >>> >>> ? ? ? ? ? ? ras to voxel transform: >>> >>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000? -0.0000? -0.0000 ? >>> 127.0000 >>> >>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? -0.0000? -1.0000 ? >>> 132.7185 >>> >>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000 ? 1.0000? -0.0000? ? >>> 90.5000 >>> >>> ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? -0.0000? -0.0000 ? ? >>> 1.0000 >>> >>> >>> ? ? ? ? ? ? Is there any other way to resolve this issue >>> than >>> ? ? ? ? ? ? reconstruction the brain again and doing all the >>> ? ? ? ? ? ? edits all over again hoping >>> ? ? ? ? ? ? that the?brain mask does not get corrupted this >>> ? ? ? ? ? ? time? >>> >>> ? ? ? ? ? ? Appreciate any help with this. >>> >>> ? ? ? ? ? ? Best, >>> ? ? ? ? ? ? Srishti >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >>> >>> >> ------------------------------ >> >> Message: 8 >> Date: Thu, 5 Apr 2018 12:41:49 -0400 >> From: srishti goel <23srishtig...@gmail.com> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <CAGqM=ZhW7-+qbR3szJv+znAPa=ZVZ9Npexz4Fu2=frnsijb...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Should I re-run the recon-all after running the last command from >> recon-all.cmd? >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> >>> Hi Srishti >>> >>> if you look in the subject's scripts dir there should be a file named >>> "recon-all.cmd". Try rerunning the last command in it (probably from the >>> mri dir) >>> >>> >>> cheers >>> Bruce >>> On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> I am sorry, I am not sure what do you mean by running the command line >>>> directly? >>>> I use the following command: >>>> >>>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user >>>> srish...@email.unc.edu --wrap "export >>>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >>>> recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa" >>>> >>>> >>>> where sbatch..... until export is our local server submission command >>>> and >>>> I run this command from the command line itself, not >>>> using any script. >>>> >>>> >>>> Best, >>>> Srishti >>>> Social/Clinical Research Specialist >>>> Child Imaging Research and Life Experiences Lab >>>> University of North Carolina at Chapel Hill >>>> email (W): srish...@email.unc.edu >>>> skype: srishti.goel12 >>>> >>>> >>>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl >>>> <fis...@nmr.mgh.harvard.edu> >>>> wrote: >>>> if you run the command that failed again on the command line >>>> directly (that is, not in recon-all) does it fail >>>> again? >>>> >>>> On Thu, 5 Apr 2018, srishti goel wrote: >>>> >>>> Hi Bruce, >>>> >>>> The machine definitely hasn't run out of memory. Here is >>>> the >>>> memory usage >>>> from recon-all.log >>>> >>>> total used free >>>> >>>> shared buff/cache available >>>> Mem: 263726968 34330048 152102696 12944 >>>> 77294224 >>>> 191963372 >>>> Swap: 2097148 0 2097148 >>>> >>>> >>>> >>>> >>>> Best, >>>> Srishti >>>> Social/Clinical Research Specialist >>>> Child Imaging Research and Life Experiences Lab >>>> University of North Carolina at Chapel Hill >>>> email (W): srish...@email.unc.edu >>>> skype: srishti.goel12 >>>> >>>> >>>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl < >>>> fis...@nmr.mgh.harvard.edu> >>>> wrote: >>>> Hi Srishti >>>> >>>> are you sure that your machine didn't just run out of >>>> memory? >>>> The recon-all.log file includes the amount of free >>>> (and >>>> total) >>>> memory at the time the process was started. >>>> >>>> cheers >>>> Bruce >>>> >>>> On Thu, 5 Apr 2018, srishti goel wrote: >>>> >>>> Hi, >>>> I have been trying to edit structural brains >>>> and >>>> very few times I would get the following error >>>> while >>>> running recon-all -s >>>> subjID >>>> >>>> white matter peak found at 110 >>>> cannot allocate memory >>>> >>>> Upon looking at the archive, there was only one >>>> similar issue and it was recommend to check >>>> mri_info >>>> as the brain mask might >>>> have been corrupted. I did that and here is the >>>> output: >>>> >>>> Volume information for brainmask.mgz >>>> >>>> type: MGH >>>> >>>> dimensions: 256 x 256 x 256 >>>> >>>> voxel sizes: 1.000000, 1.000000, 1.000000 >>>> >>>> type: UCHAR (0) >>>> >>>> fov: 256.000 >>>> >>>> dof: 0 >>>> >>>> xstart: -128.0, xend: 128.0 >>>> >>>> ystart: -128.0, yend: 128.0 >>>> >>>> zstart: -128.0, zend: 128.0 >>>> >>>> TR: 0.00 msec, TE: 0.00 msec, TI: >>>> 0.00 >>>> msec, flip angle: 0.00 degrees >>>> >>>> nframes: 1 >>>> >>>> PhEncDir: UNKNOWN >>>> >>>> FieldStrength: 0.000000 >>>> >>>> ras xform present >>>> >>>> xform info: x_r = -1.0000, y_r = 0.0000, >>>> z_r >>>> = 0.0000, c_r = -1.0000 >>>> >>>> : x_a = 0.0000, y_a = 0.0000, >>>> z_a >>>> = 1.0000, c_a = 37.5000 >>>> >>>> : x_s = 0.0000, y_s = -1.0000, >>>> z_s >>>> = 0.0000, c_s = 4.7185 >>>> >>>> >>>> talairach xfm :/pine/scr/s/r/srishtig/Duke_T >>>> est/Freesurfer_out/11039/mri/transforms/talair >>>> ach.xfm >>>> >>>> Orientation : LIA >>>> >>>> Primary Slice Direction: coronal >>>> >>>> >>>> voxel to ras transform: >>>> >>>> -1.0000 0.0000 0.0000 >>>> 127.0000 >>>> >>>> 0.0000 0.0000 1.0000 >>>> -90.5000 >>>> >>>> 0.0000 -1.0000 0.0000 >>>> 132.7185 >>>> >>>> 0.0000 0.0000 0.0000 >>>> 1.0000 >>>> >>>> >>>> voxel-to-ras determinant -1 >>>> >>>> >>>> ras to voxel transform: >>>> >>>> -1.0000 -0.0000 -0.0000 >>>> 127.0000 >>>> >>>> -0.0000 -0.0000 -1.0000 >>>> 132.7185 >>>> >>>> -0.0000 1.0000 -0.0000 >>>> 90.5000 >>>> >>>> -0.0000 -0.0000 -0.0000 >>>> 1.0000 >>>> >>>> >>>> Is there any other way to resolve this issue >>>> than >>>> reconstruction the brain again and doing all >>>> the >>>> edits all over again hoping >>>> that the brain mask does not get corrupted this >>>> time? >>>> >>>> Appreciate any help with this. >>>> >>>> Best, >>>> Srishti >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the >>>> person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in >>>> error and the >>>> e-mail >>>> contains patient information, please contact the Partners >>>> Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was >>>> sent to you >>>> in error >>>> but does not contain patient information, please contact >>>> the >>>> sender >>>> and properly >>>> dispose of the e-mail. >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 652c7921/attachment-0001.html >> >> ------------------------------ >> >> Message: 9 >> Date: Thu, 5 Apr 2018 12:43:22 -0400 (EDT) >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <alpine.lrh.2.21.1804051243000.18...@tiamat.nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> let's see if it works. If it does, you should be able to run >> >> recon-all -s SUBJID -make all >> >> cheers >> Bruce >> >> >> On Thu, 5 Apr 2018, srishti goel wrote: >> >>> Should I re-run the recon-all after running the last command from >>> recon-all.cmd? >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> Hi Srishti >>> >>> if you look in the subject's scripts dir there should be a file >>> named "recon-all.cmd". Try rerunning the last >>> command in it (probably from the mri dir) >>> >>> cheers >>> Bruce >>> On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> I am sorry, I am not sure what do you mean by running the >>> command line directly? >>> I use the following command: >>> >>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user >>> srish...@email.unc.edu --wrap "export >>> >>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >>> recon-all -s 13166 >>> -autorecon2-cp -autorecon3 -nowmsa" >>> >>> >>> where sbatch..... until export is our local server >>> submission command and I run this command from the >>> command line itself, not >>> using any script. >>> >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> ? ? ? if you run the command that failed again on the >>> command line directly (that is, not in >>> recon-all) does it fail >>> ? ? ? again? >>> >>> ? ? ? On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> ? ? ? ? ? ? Hi Bruce, >>> >>> ? ? ? ? ? ? The machine definitely hasn't run out of >>> memory. Here is the memory usage >>> ? ? ? ? ? ? from recon-all.log ? >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ? ? ?used ? >>> ? ? ?free ? ? ? ? ? ? ? ? ? >>> ? ? ? ? ? ? shared ?buff/cache ? available >>> ? ? ? ? ? ? Mem: ? ? ?263726968 ? ?34330048 ? 152102696 ? ? >>> ? 12944 ? ?77294224 ? >>> ? ? ? ? ? ? 191963372 >>> ? ? ? ? ? ? Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ? ? ? ? ? >>> 2097148 >>> >>> >>> >>> >>> ? ? ? ? ? ? Best, >>> ? ? ? ? ? ? Srishti >>> ? ? ? ? ? ? Social/Clinical Research Specialist >>> ? ? ? ? ? ? Child Imaging Research and Life Experiences Lab >>> ? ? ? ? ? ? University of North Carolina at Chapel Hill >>> ? ? ? ? ? ? email (W): srish...@email.unc.edu >>> ? ? ? ? ? ? skype: srishti.goel12 >>> >>> >>> ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> >>> ? ? ? ? ? ? wrote: >>> ? ? ? ? ? ? ? ? ? Hi Srishti >>> >>> ? ? ? ? ? ? ? ? ? are you sure that your machine didn't >>> just run out of memory? >>> ? ? ? ? ? ? ? ? ? The recon-all.log file includes the >>> amount of free (and total) >>> ? ? ? ? ? ? ? ? ? memory at the time the process was >>> started. >>> >>> ? ? ? ? ? ? ? ? ? cheers >>> ? ? ? ? ? ? ? ? ? Bruce >>> >>> ? ? ? ? ? ? ? ? ? ?On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Hi, >>> ? ? ? ? ? ? ? ? ? ? ? ? I have been trying to edit >>> structural brains and >>> ? ? ? ? ? ? ? ? ? ? ? ? very few times I would get the >>> following error while >>> ? ? ? ? ? ? ? ? ? ? ? ? running recon-all -s >>> ? ? ? ? ? ? ? ? ? ? ? ? subjID >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? white matter peak found at 110 >>> ? ? ? ? ? ? ? ? ? ? ? ? cannot allocate memory >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Upon looking at the archive, there >>> was only one >>> ? ? ? ? ? ? ? ? ? ? ? ? similar issue and it was recommend >>> to check mri_info >>> ? ? ? ? ? ? ? ? ? ? ? ? as the brain mask might >>> ? ? ? ? ? ? ? ? ? ? ? ? have been corrupted. I did that and >>> here is the >>> ? ? ? ? ? ? ? ? ? ? ? ? output: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Volume information for brainmask.mgz >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: MGH >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? dimensions: 256 x 256 x 256 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? voxel sizes: 1.000000, 1.000000, >>> 1.000000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: UCHAR (0) >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? fov: 256.000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? dof: 0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? xstart: -128.0, xend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ystart: -128.0, yend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? zstart: -128.0, zend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? TR: 0.00 msec, TE: 0.00 >>> msec, TI: 0.00 >>> ? ? ? ? ? ? ? ? ? ? ? ? msec, flip angle: 0.00 degrees >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? nframes: 1 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? PhEncDir: UNKNOWN >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? FieldStrength: 0.000000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ras xform present >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? xform info: x_r =? -1.0000, y_r >>> = ? 0.0000, z_r >>> ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_r =? ? -1.0000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_a = ? 0.0000, y_a >>> = ? 0.0000, z_a >>> ? ? ? ? ? ? ? ? ? ? ? ? = ? 1.0000, c_a =? ? 37.5000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_s = ? 0.0000, y_s >>> =? -1.0000, z_s >>> ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_s = ? ? 4.7185 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? talairach xfm >>> >>> :/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/tal >>> air >>> ? ? ? ? ? ? ? ? ? ? ? ? ach.xfm >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Orientation ? : LIA >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Primary Slice Direction: coronal >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? voxel to ras transform: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000 ? 0.0000 ? >>> 0.0000 ? 127.0000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? >>> 1.0000 ? -90.5000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000? -1.0000 ? >>> 0.0000 ? 132.7185 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 ? 0.0000 ? >>> 0.0000 ? ? 1.0000 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? voxel-to-ras determinant -1 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ras to voxel transform: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000? -0.0000? >>> -0.0000 ? 127.0000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? -0.0000? >>> -1.0000 ? 132.7185 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000 ? 1.0000? >>> -0.0000? ? 90.5000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? -0.0000? >>> -0.0000 ? ? 1.0000 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Is there any other way to resolve >>> this issue than >>> ? ? ? ? ? ? ? ? ? ? ? ? reconstruction the brain again and >>> doing all the >>> ? ? ? ? ? ? ? ? ? ? ? ? edits all over again hoping >>> ? ? ? ? ? ? ? ? ? ? ? ? that the?brain mask does not get >>> corrupted this >>> ? ? ? ? ? ? ? ? ? ? ? ? time? >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Appreciate any help with this. >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Best, >>> ? ? ? ? ? ? ? ? ? ? ? ? Srishti >>> >>> >>> ? ? ? ? ? ? _______________________________________________ >>> ? ? ? ? ? ? Freesurfer mailing list >>> ? ? ? ? ? ? Freesurfer@nmr.mgh.harvard.edu >>> ? ? ? ? ? ? >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ? ? ? ? ? ? The information in this e-mail is intended only >>> for the person to whom >>> ? ? ? ? ? ? it is >>> ? ? ? ? ? ? addressed. If you believe this e-mail was sent >>> to you in error and the >>> ? ? ? ? ? ? e-mail >>> ? ? ? ? ? ? contains patient information, please contact >>> the Partners Compliance >>> ? ? ? ? ? ? HelpLine at >>> ? ? ? ? ? ? http://www.partners.org/complianceline . If the >>> e-mail was sent to you >>> ? ? ? ? ? ? in error >>> ? ? ? ? ? ? but does not contain patient information, >>> please contact the sender >>> ? ? ? ? ? ? and properly >>> ? ? ? ? ? ? dispose of the e-mail. >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the >>> person to whom it is >>> addressed. If you believe this e-mail was sent to you in >>> error and the e-mail >>> contains patient information, please contact the Partners >>> Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was >>> sent to you in error >>> but does not contain patient information, please contact >>> the sender and properly >>> dispose of the e-mail. >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>> >> ------------------------------ >> >> Message: 10 >> Date: Thu, 5 Apr 2018 12:46:40 -0400 >> From: srishti goel <23srishtig...@gmail.com> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <CAGqM=zi0ousz8xx5+olejhh_8xknnhjsoem48qogydhhyh3...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> So it gave this error: >> >> 3d normalization pass 1 of 2 >> >> white matter peak found at 110 >> >> HISTOalloc(-2147483648): could not allocate histogram >> >> Cannot allocate memory >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> >>> let's see if it works. If it does, you should be able to run >>> >>> recon-all -s SUBJID -make all >>> >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> Should I re-run the recon-all after running the last command from >>>> recon-all.cmd? >>>> >>>> Best, >>>> Srishti >>>> Social/Clinical Research Specialist >>>> Child Imaging Research and Life Experiences Lab >>>> University of North Carolina at Chapel Hill >>>> email (W): srish...@email.unc.edu >>>> skype: srishti.goel12 >>>> >>>> >>>> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl >>>> <fis...@nmr.mgh.harvard.edu> >>>> wrote: >>>> Hi Srishti >>>> >>>> if you look in the subject's scripts dir there should be a file >>>> named "recon-all.cmd". Try rerunning the last >>>> command in it (probably from the mri dir) >>>> >>>> cheers >>>> Bruce >>>> On Thu, 5 Apr 2018, srishti goel wrote: >>>> >>>> I am sorry, I am not sure what do you mean by running the >>>> command line directly? >>>> I use the following command: >>>> >>>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user >>>> srish...@email.unc.edu --wrap "export >>>> >>>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >>>> recon-all -s 13166 >>>> -autorecon2-cp -autorecon3 -nowmsa" >>>> >>>> >>>> where sbatch..... until export is our local server >>>> submission >>>> command and I run this command from the >>>> command line itself, not >>>> using any script. >>>> >>>> >>>> Best, >>>> Srishti >>>> Social/Clinical Research Specialist >>>> Child Imaging Research and Life Experiences Lab >>>> University of North Carolina at Chapel Hill >>>> email (W): srish...@email.unc.edu >>>> skype: srishti.goel12 >>>> >>>> >>>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl < >>>> fis...@nmr.mgh.harvard.edu> wrote: >>>> if you run the command that failed again on the >>>> command >>>> line directly (that is, not in >>>> recon-all) does it fail >>>> again? >>>> >>>> On Thu, 5 Apr 2018, srishti goel wrote: >>>> >>>> Hi Bruce, >>>> >>>> The machine definitely hasn't run out of >>>> memory. >>>> Here is the memory usage >>>> from recon-all.log >>>> >>>> total used >>>> free >>>> shared buff/cache available >>>> Mem: 263726968 34330048 152102696 >>>> 12944 77294224 >>>> 191963372 >>>> Swap: 2097148 0 >>>> 2097148 >>>> >>>> >>>> >>>> >>>> Best, >>>> Srishti >>>> Social/Clinical Research Specialist >>>> Child Imaging Research and Life Experiences Lab >>>> University of North Carolina at Chapel Hill >>>> email (W): srish...@email.unc.edu >>>> skype: srishti.goel12 >>>> >>>> >>>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl < >>>> fis...@nmr.mgh.harvard.edu> >>>> wrote: >>>> Hi Srishti >>>> >>>> are you sure that your machine didn't >>>> just >>>> run out of memory? >>>> The recon-all.log file includes the >>>> amount >>>> of free (and total) >>>> memory at the time the process was >>>> started. >>>> >>>> cheers >>>> Bruce >>>> >>>> On Thu, 5 Apr 2018, srishti goel wrote: >>>> >>>> Hi, >>>> I have been trying to edit >>>> structural >>>> brains and >>>> very few times I would get the >>>> following error while >>>> running recon-all -s >>>> subjID >>>> >>>> white matter peak found at 110 >>>> cannot allocate memory >>>> >>>> Upon looking at the archive, there >>>> was only one >>>> similar issue and it was recommend >>>> to >>>> check mri_info >>>> as the brain mask might >>>> have been corrupted. I did that and >>>> here is the >>>> output: >>>> >>>> Volume information for >>>> brainmask.mgz >>>> >>>> type: MGH >>>> >>>> dimensions: 256 x 256 x 256 >>>> >>>> voxel sizes: 1.000000, 1.000000, >>>> 1.000000 >>>> >>>> type: UCHAR (0) >>>> >>>> fov: 256.000 >>>> >>>> dof: 0 >>>> >>>> xstart: -128.0, xend: 128.0 >>>> >>>> ystart: -128.0, yend: 128.0 >>>> >>>> zstart: -128.0, zend: 128.0 >>>> >>>> TR: 0.00 msec, TE: 0.00 >>>> msec, TI: 0.00 >>>> msec, flip angle: 0.00 degrees >>>> >>>> nframes: 1 >>>> >>>> PhEncDir: UNKNOWN >>>> >>>> FieldStrength: 0.000000 >>>> >>>> ras xform present >>>> >>>> xform info: x_r = -1.0000, >>>> y_r = >>>> 0.0000, z_r >>>> = 0.0000, c_r = -1.0000 >>>> >>>> : x_a = 0.0000, >>>> y_a = >>>> 0.0000, z_a >>>> = 1.0000, c_a = 37.5000 >>>> >>>> : x_s = 0.0000, y_s >>>> = -1.0000, z_s >>>> = 0.0000, c_s = 4.7185 >>>> >>>> >>>> talairach xfm >>>> >>>> :/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/t >>>> ransforms/talair >>>> ach.xfm >>>> >>>> Orientation : LIA >>>> >>>> Primary Slice Direction: coronal >>>> >>>> >>>> voxel to ras transform: >>>> >>>> -1.0000 0.0000 >>>> 0.0000 127.0000 >>>> >>>> 0.0000 0.0000 >>>> 1.0000 -90.5000 >>>> >>>> 0.0000 -1.0000 >>>> 0.0000 132.7185 >>>> >>>> 0.0000 0.0000 >>>> 0.0000 1.0000 >>>> >>>> >>>> voxel-to-ras determinant -1 >>>> >>>> >>>> ras to voxel transform: >>>> >>>> -1.0000 -0.0000 >>>> -0.0000 127.0000 >>>> >>>> -0.0000 -0.0000 >>>> -1.0000 132.7185 >>>> >>>> -0.0000 1.0000 >>>> -0.0000 90.5000 >>>> >>>> -0.0000 -0.0000 >>>> -0.0000 1.0000 >>>> >>>> >>>> Is there any other way to resolve >>>> this issue than >>>> reconstruction the brain again and >>>> doing all the >>>> edits all over again hoping >>>> that the brain mask does not get >>>> corrupted this >>>> time? >>>> >>>> Appreciate any help with this. >>>> >>>> Best, >>>> Srishti >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.e >>>> du/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only >>>> for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent >>>> to >>>> you in error and the >>>> e-mail >>>> contains patient information, please contact >>>> the >>>> Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the >>>> e-mail was sent to you >>>> in error >>>> but does not contain patient information, >>>> please >>>> contact the sender >>>> and properly >>>> dispose of the e-mail. >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the >>>> person to whom it is >>>> addressed. If you believe this e-mail was sent to you in >>>> error and the e-mail >>>> contains patient information, please contact the Partners >>>> Compliance HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was >>>> sent to you in error >>>> but does not contain patient information, please contact >>>> the >>>> sender and properly >>>> dispose of the e-mail. >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer 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. >>> >>> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 5cd48b42/attachment-0001.html >> >> ------------------------------ >> >> Message: 11 >> Date: Thu, 5 Apr 2018 12:48:08 -0400 (EDT) >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter >> peak at 110, cannot allocate memory) >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <alpine.lrh.2.21.1804051247570.18...@tiamat.nmr.mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> can you email us the input file and the full command line you ran? >> On Thu, 5 >> Apr 2018, srishti goel wrote: >> >>> So it gave this error: >>> >>> 3d normalization pass 1 of 2 >>> >>> white matter peak found at 110 >>> >>> HISTOalloc(-2147483648): could not allocate histogram >>> >>> Cannot allocate memory >>> >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> let's see if it works. If it does, you should be able to run >>> >>> recon-all -s SUBJID -make all >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> Should I re-run the recon-all after running the last >>> command from recon-all.cmd? >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> ? ? ? Hi Srishti >>> >>> ? ? ? if you look in the subject's scripts dir there should >>> be a file named "recon-all.cmd". Try >>> rerunning the last >>> ? ? ? command in it (probably from the mri dir) >>> >>> ? ? ? cheers >>> ? ? ? Bruce >>> ? ? ? On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> ? ? ? ? ? ? I am sorry, I am not sure what do you mean by >>> running the command line directly? >>> ? ? ? ? ? ? I use the following command: >>> >>> ? ? ? ? ? ? sbatch --mem 2200 -t 6-00:00 --mail-type END >>> --mail-user srish...@email.unc.edu --wrap >>> "export >>> ? ? ? ? ? ? >>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; >>> recon-all -s 13166 >>> ? ? ? ? ? ? -autorecon2-cp -autorecon3 -nowmsa" >>> >>> >>> ? ? ? ? ? ? where sbatch..... until export is our local >>> server submission command and I run this >>> command from the >>> ? ? ? ? ? ? command line itself, not >>> ? ? ? ? ? ? using any script. >>> >>> >>> ? ? ? ? ? ? Best, >>> ? ? ? ? ? ? Srishti >>> ? ? ? ? ? ? Social/Clinical Research Specialist >>> ? ? ? ? ? ? Child Imaging Research and Life Experiences Lab >>> ? ? ? ? ? ? University of North Carolina at Chapel Hill >>> ? ? ? ? ? ? email (W): srish...@email.unc.edu >>> ? ? ? ? ? ? skype: srishti.goel12 >>> >>> >>> ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> ? ? ? ? ? ? ? ? ? if you run the command that failed again >>> on the command line directly (that is, not >>> in >>> ? ? ? ? ? ? recon-all) does it fail >>> ? ? ? ? ? ? ? ? ? again? >>> >>> ? ? ? ? ? ? ? ? ? On Thu, 5 Apr 2018, srishti goel wrote: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Hi Bruce, >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? The machine definitely hasn't run >>> out of memory. Here is the memory usage >>> ? ? ? ? ? ? ? ? ? ? ? ? from recon-all.log ? >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? >>> ? ? ?used ? ? ? ?free ? ? ? ? ? ? ? ? ? >>> ? ? ? ? ? ? ? ? ? ? ? ? shared ?buff/cache ? available >>> ? ? ? ? ? ? ? ? ? ? ? ? Mem: ? ? ?263726968 ? ?34330048 ? >>> 152102696 ? ? ? 12944 ? ?77294224 ? >>> ? ? ? ? ? ? ? ? ? ? ? ? 191963372 >>> ? ? ? ? ? ? ? ? ? ? ? ? Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ? >>> ? ? ? ? 2097148 >>> >>> >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? Best, >>> ? ? ? ? ? ? ? ? ? ? ? ? Srishti >>> ? ? ? ? ? ? ? ? ? ? ? ? Social/Clinical Research Specialist >>> ? ? ? ? ? ? ? ? ? ? ? ? Child Imaging Research and Life >>> Experiences Lab >>> ? ? ? ? ? ? ? ? ? ? ? ? University of North Carolina at >>> Chapel Hill >>> ? ? ? ? ? ? ? ? ? ? ? ? email (W): srish...@email.unc.edu >>> ? ? ? ? ? ? ? ? ? ? ? ? skype: srishti.goel12 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:16 PM, >>> Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> ? ? ? ? ? ? ? ? ? ? ? ? wrote: >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi Srishti >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? are you sure that your >>> machine didn't just run out of memory? >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? The recon-all.log file >>> includes the amount of free (and total) >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? memory at the time the >>> process was started. >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? cheers >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Bruce >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?On Thu, 5 Apr 2018, srishti >>> goel wrote: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Hi, >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? I have been trying to >>> edit structural brains and >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? very few times I would >>> get the following error while >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? running recon-all -s >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? subjID >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? white matter peak found >>> at 110 >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? cannot allocate memory >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Upon looking at the >>> archive, there was only one >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? similar issue and it >>> was recommend to check mri_info >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? as the brain mask might >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? have been corrupted. I >>> did that and here is the >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? output: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Volume information for >>> brainmask.mgz >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: MGH >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? dimensions: 256 x >>> 256 x 256 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? voxel sizes: >>> 1.000000, 1.000000, 1.000000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? type: UCHAR >>> (0) >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? fov: 256.000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? dof: 0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? xstart: -128.0, >>> xend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ystart: -128.0, >>> yend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? zstart: -128.0, >>> zend: 128.0 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? TR: 0.00 >>> msec, TE: 0.00 msec, TI: 0.00 >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? msec, flip angle: 0.00 >>> degrees >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? nframes: 1 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? PhEncDir: UNKNOWN >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? FieldStrength: >>> 0.000000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ras xform present >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? xform info: x_r =? >>> -1.0000, y_r = ? 0.0000, z_r >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_r =? ? >>> -1.0000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_a = ? >>> 0.0000, y_a = ? 0.0000, z_a >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 1.0000, c_a =? ? >>> 37.5000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? : x_s = ? >>> 0.0000, y_s =? -1.0000, z_s >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = ? 0.0000, c_s = ? ? >>> 4.7185 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? talairach xfm >>> ? ? ? ? ? ? >>> :/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/tal >>> air >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ach.xfm >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Orientation ? : LIA >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Primary Slice >>> Direction: coronal >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? voxel to ras transform: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000 >>> ? 0.0000 ? 0.0000 ? 127.0000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 >>> ? 0.0000 ? 1.0000 ? -90.5000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000? >>> -1.0000 ? 0.0000 ? 132.7185 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.0000 >>> ? 0.0000 ? 0.0000 ? ? 1.0000 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? voxel-to-ras >>> determinant -1 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ras to voxel transform: >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -1.0000? >>> -0.0000? -0.0000 ? 127.0000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? >>> -0.0000? -1.0000 ? 132.7185 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000 >>> ? 1.0000? -0.0000? ? 90.5000 >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? ? ? ? ? ? ? -0.0000? >>> -0.0000? -0.0000 ? ? 1.0000 >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Is there any other way >>> to resolve this issue than >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? reconstruction the >>> brain again and doing all the >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? edits all over again >>> hoping >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? that the?brain mask >>> does not get corrupted this >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? time? >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Appreciate any help >>> with this. >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Best, >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? Srishti >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? >>> _______________________________________________ >>> ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer mailing list >>> ? ? ? ? ? ? ? ? ? ? ? ? Freesurfer@nmr.mgh.harvard.edu >>> ? ? ? ? ? ? ? ? ? ? ? ? >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? The information in this e-mail is >>> intended only for the person to whom >>> ? ? ? ? ? ? ? ? ? ? ? ? it is >>> ? ? ? ? ? ? ? ? ? ? ? ? addressed. If you believe this >>> e-mail was sent to you in error and the >>> ? ? ? ? ? ? ? ? ? ? ? ? e-mail >>> ? ? ? ? ? ? ? ? ? ? ? ? contains patient information, >>> please contact the Partners Compliance >>> ? ? ? ? ? ? ? ? ? ? ? ? HelpLine at >>> ? ? ? ? ? ? ? ? ? ? ? ? >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> ? ? ? ? ? ? ? ? ? ? ? ? in error >>> ? ? ? ? ? ? ? ? ? ? ? ? but does not contain patient >>> information, please contact the sender >>> ? ? ? ? ? ? ? ? ? ? ? ? and properly >>> ? ? ? ? ? ? ? ? ? ? ? ? dispose of the e-mail. >>> >>> >>> >>> >>> ? ? ? ? ? ? _______________________________________________ >>> ? ? ? ? ? ? Freesurfer mailing list >>> ? ? ? ? ? ? Freesurfer@nmr.mgh.harvard.edu >>> ? ? ? ? ? ? >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ? ? ? ? ? ? The information in this e-mail is intended only >>> for the person to whom it is >>> ? ? ? ? ? ? addressed. If you believe this e-mail was sent >>> to you in error and the e-mail >>> ? ? ? ? ? ? contains patient information, please contact >>> the Partners Compliance HelpLine at >>> ? ? ? ? ? ? http://www.partners.org/complianceline . If the >>> e-mail was sent to you in error >>> ? ? ? ? ? ? but does not contain patient information, >>> please contact the sender and properly >>> ? ? ? ? ? ? dispose of the e-mail. >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the >>> person to whom it is >>> addressed. If you believe this e-mail was sent to you in >>> error and the e-mail >>> contains patient information, please contact the Partners >>> Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was >>> sent to you in error >>> but does not contain patient information, please contact >>> the sender and properly >>> dispose of the e-mail. >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer 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. >>> >>> >>> >>> >> ------------------------------ >> >> Message: 12 >> Date: Thu, 5 Apr 2018 12:49:49 -0400 >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] mri_vol2surf: unable to compare volume maps >> To: <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <6bb974cb-7874-6541-ee7c-b635d3037...@mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8"; format=flowed >> >> Those commands look ok. My suspicion goes to the use of --regheader. See >> whether the registration is ok with >> >> tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s >> mni152_subject --surfs --reg reg.deleteme.dat >> >> >> On 04/05/2018 08:34 AM, srishti goel wrote: >>> Hi, >>> >>> I am trying to compare my volume maps >>> (negative_allsocial_proportion.nii) to someone else's >>> (SN_like_cortical_lh.nii.gz) who have it on a surface >>> (mni152_subject). So I used the steps for mri_vol2surf command as >>> follows: >>> >>> Commands: >>> mri_vol2surf --src negative_allsocial_proportion.nii --regheader >>> mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 >>> Then to view it: >>> tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii >>> -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5 >>> >>> Everything ran fine and we didn't get any error but then while viewing >>> the files we could not see our map (neg_allsocail_lh.nii) on the >>> surface. This file seemed to work fine as it is not an empty file when >>> I checked the file size. However, when we view it using tksurfer it >>> does not show up as a highlighted portion on the surface. The >>> SN_like_cortical_lh.nii.gz file shows up just fine. >>> >>> Could someone please help me figure out what might have gone wrong here. >>> >>> Thanks so much! >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ------------------------------ >> >> Message: 13 >> Date: Thu, 5 Apr 2018 12:59:16 -0400 >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] scan log generated by dcmunpack >> To: <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <22ecfa88-e463-169b-03c5-4c25ac224...@mgh.harvard.edu> >> Content-Type: text/plain; charset="windows-1252"; format=flowed >> >> It looks like there is something wrong with that dicom file/series >> because the pixel spacing is "unknown". Where did the dicoms from from? >> Have they been anonymized? >> >> >> On 04/05/2018 12:12 PM, Kan Ding wrote: >>> Hello: >>> >>> I am trying to unpack my DICOM folder and run recon-all. After >>> dcmunpack, I selected 301 to run recon-all. But the recon-all didn?t >>> go through. Please see the attached scan.log, recon-all.log, >>> error.log, and the pic of my DICOM folder. >>> >>> Thank you so much. >>> >>> Kan Ding, MD >>> >>> Assistant Professor- Department of Neurology and Neurotherapeutics >>> >>> UT Southwestern Medical Center at Dallas >>> >>> Tel: 214-648-9197 >>> >>> Fax: 214-648-6320 >>> >>> >>> ------------------------------------------------------------------------ >>> >>> UTSouthwestern >>> >>> Medical Center >>> >>> >>> The future of medicine, today. >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ------------------------------ >> >> Message: 14 >> Date: Thu, 5 Apr 2018 17:49:11 +0000 >> From: "Crawford, Anna" <crawf...@ccf.org> >> Subject: [Freesurfer] Time Series to Surface >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <1522950551835.87...@ccf.org> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hello, >> >> I have a time series (.hdr/.img) that I want to overlay onto a surface, >> specifically the inflated surface from the anatomy. I suspect I have to >> use mri_vol2surf, which requires a source registration file. How do I get >> this file? Then once I have this file, will I be able to view step by >> step through the time series on the inflated volume? >> >> Thanks for your help, >> Anna >> >> >> >> =================================== >> >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is currently ranked as the No. 2 hospital in the country >> by U.S. News & World Report (2017-2018). Visit us online at >> http://www.clevelandclinic.org for a complete listing of our services, >> staff and locations. Confidentiality Note: This message is intended for >> use only by the individual or entity to which it is addressed and may >> contain information that is privileged, confidential, and exempt from >> disclosure under applicable law. If the reader of this message is not the >> intended recipient or the employee or agent responsible for delivering >> the message to the intended recipient, you are hereby notified that any >> dissemination, distribution or copying of this communication is strictly >> prohibited. If you have received this communication in error, please >> contact the sender immediately and destroy the material in its entirety, >> whether electronic or hard copy. Thank you. >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 10774d4e/attachment-0001.html >> >> ------------------------------ >> >> Message: 15 >> Date: Thu, 5 Apr 2018 19:21:18 +0000 >> From: "Lussier,Desiree" <desiree.luss...@ufl.edu> >> Subject: [Freesurfer] Tracula - Could not find satisfactory control >> point fit >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> >> <bn6pr22mb0228f1c6a278da29232cc6c3ff...@bn6pr22mb0228.namprd22.prod.outlo >> ok.com> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear Freesurfer experts, >> >> >> I have been trying run trac-all -prep on two subjects but it seems to be >> stuck on the priors pathway estimation. The following (with updated >> number of tries) keeps appearing in the terminal: >> >> >> WARN: Could not find satisfactory control point fit - try 288 >> Finding center streamline >> INFO: Step is 5 voxels >> WARN: Turning off deviation check for center streamline >> INFO: Step is 5 voxels >> WARN: Turning off FA check for center streamline >> INFO: Step is 5 voxels >> >> >> I've attached the log here. Previous communications I've seen regarding >> this are years old and were solved by upgrading to 5.3. However, I'm >> already using the 64 bit 6.0. >> >> >> Advice regarding this situation would be greatly appreciated. >> >> >> Thank you, >> >> Desiree Lussier >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 6ea26451/attachment.html >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: trac-all.log >> Type: text/x-log >> Size: 525522 bytes >> Desc: trac-all.log >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180405/ >> 6ea26451/attachment.bin >> >> ------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> End of Freesurfer Digest, Vol 170, Issue 7 >> ****************************************** > > > > > ------------------------------------------------------------------------- > This message was secured by ZixCorp(R). > > > _______________________________________________ > 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
