Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

Tracula - Could not find satisfactory control point fit
by Lussier,Desiree 06 Apr '18

06 Apr '18

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

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Re: [Freesurfer] scan log generated by dcmunpack
by Kan Ding 05 Apr '18

05 Apr '18

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" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] scan log generated by dcmunpack To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <22ecfa88-e463-169b-03c5-4c25ac2244db(a)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-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu" <reesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu> wrote: >Send Freesurfer mailing list submissions to > freesurfer(a)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-request(a)nmr.mgh.harvard.edu > >You can reach the person managing the list at > freesurfer-owner(a)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.Ding(a)utsouthwestern.edu> >Subject: [Freesurfer] scan log generated by dcmunpack >To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: <D6EBC339.10FF3%kan.ding(a)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. > >

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scan log generated by dcmunpack
by Kan Ding 05 Apr '18

05 Apr '18

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 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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recon-all: exited with errors (white matter peak at 110, cannot allocate memory)
by srishti goel 05 Apr '18

05 Apr '18

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/talairach.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

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Qdec+Table format issue ?????
by Dimitrios Trifonopoulos 05 Apr '18

05 Apr '18

Dear Recipient, I am a Master 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 text editors (mac text editor, gedit and text wrangler) however I end up in 2 different errors without be able 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' to 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:subjects SLMAC14$ long_mris_slopes --qdec /Applications/freesurfer/subjects/qdec/lala copy.dat.doc --meas thickness --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/qdec/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 understand 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

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Re: [Freesurfer] query regarding creating an atlas from nifti volumes.
by Bruce Fischl 05 Apr '18

05 Apr '18

Hi Mageshwar gcs is a surface-based format for cortical segmentation. And it wouldn't be a conversion as much as it would be a training. If you can sample your regions onto the surface in .annot format you can use mris_ca_train to build a new gcs that you can then apply with mris_ca_label cheers Bruce On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote: > Dear Bruce, > > We would like to use a probabilistic atlas built upon by us (with 170 regions) on top of the harvard > oxford atlas and would like to use this extended atlas to perform segmentation and analysis on > freesurfer. We have these 170 regions in 170 different nifti files. I would like to know if we could > use these regions in .nii or .mgz format and convert it to gcs format. > > Thank you for your help, > > > Kind regards > Mageshwar Selvakumar, M.Sc > Department of Pharmakologische Bildgebung und Bildanalyse > Friedrich Alexander Universität Erlangen Nürnberg > > Office: Fahrstr. 17, 91054 Erlangen > Phone: + 49-9131-8522898 > > > ____________________________________________________________________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of > Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Sent: Thursday, April 5, 2018 3:35 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] query regarding creating an atlas from nifti volumes. > Hi Mageshwar > > what kind of an atlas are you talking about? We have multiple atlases for > different purposes. > > cheers > Bruce > On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote: > > > Dear All, > > > > I am a newbie to freesurfer and I would like to use our in-house built probabilistic atlas(each > > region as a binary mask and available as nifti files). I would like to create an atlas out of it > and > > use it for our analysis. On searching the previous mailing list I came across a discussion where > the > > volume information was converted into surface information and can be converted to labels and > > annotations but I couldn't find much documentation on creating an atlas directly from the volume > or > > surface information. It would be nice if someone can point me out if this is possible and some > > relevant information to continue on it. > > > > Thank you, > > > > Kind regards > > > > Mageshwar Selvakumar, M.Sc > > > > Department of Pharmakologische Bildgebung und Bildanalyse > > > > Friedrich Alexander Universität Erlangen Nürnberg > > > > > > Office: Fahrstr. 17, 91054 Erlangen > > > > Phone: + 49-9131-8522898 > > > > > > > > > >

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query regarding creating an atlas from nifti volumes.
by Mageshwar Selvakumar 05 Apr '18

05 Apr '18

Dear All, I am a newbie to freesurfer and I would like to use our in-house built probabilistic atlas(each region as a binary mask and available as nifti files). I would like to create an atlas out of it and use it for our analysis. On searching the previous mailing list I came across a discussion where the volume information was converted into surface information and can be converted to labels and annotations but I couldn't find much documentation on creating an atlas directly from the volume or surface information. It would be nice if someone can point me out if this is possible and some relevant information to continue on it. Thank you, Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898

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Re: [Freesurfer] error rerunning recon-all (exited with ERRORS)
by Anna Daniels 05 Apr '18

05 Apr '18

Hi Douglas, thank you for the quick reply! That helped for the first hard failure. Do you have any idea what could have caused the second error message? This only happened for some subjects when rerunning recon-all with -autorecon2 -autorecon3, but always resulted in this error log: Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 Cannot allocate memory Linux node098 2.6.32-696.20.1.el6.x86_64 #1 SMP Thu Jan 25 08:47:49 CST 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 44538_T1_fs_edit exited with ERRORS at Do 29. Mär 01:28:15 CEST 2018 Attached you can find the respective recon-all.log file. Thank you! Best, Anna

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Abstract submission deadline extended - 1st International Workshop on Predictive Processing
by Sanjeev Nara 05 Apr '18

05 Apr '18

Hello Researchers, We have received request from lot of researchers to extend the deadline for abstract submission, We are happy to announce that the deadline for abstract submission for 1st International Workshop on Predictive Processing (WoPP) has been extended upto 16th April 2018. Hope to see you in San Sebastian. on behalf of Organisers Sanjeev Nara Predoctoral Researcher BCBL www.bcbl.eu https://sites.google.com/view/sanjeev-nara/ Abstract submission deadline extended - 1st International Workshop on Predictive Processing We would like to inform you that the abstract submission deadline to PREDICTIVE PROCESSING has been extended. The new deadline is April 16th. The conference dates are June 20-22, 2018 Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. We invite submissions from researchers genuinely interested in discussing their data within the framework of the prediction view on neurocognition and brain functioning. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Extended until April 16th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018. BQ_BEGIN BQ_END

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MRIxfmCRS2XYZtkreg function
by Ricardo Valle 04 Apr '18

04 Apr '18

Dear Freesurfer community, I have stumbled upon a function called MRIxfmCRS2XYZtkreg in the Freesurfer source code on Github. It is used in several places but does not seem to be defined anywhere in the repository. Is it part of some external library? Would it be possible to take a look at its source? Thank you. All the best, Ruy

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Freesurfer April 2018