Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Question about visualization on the surface
by Kaveh Kohan 28 Apr '14

28 Apr '14

Dear All, This probably a newbie question, so I apologize if it is a naive one, please bear with me. I have on value for each ROI on the surface of brain and one value for each sub-cortical structures. Those ROIs and sub-cortical structures correspond to freesurfer atlas. I have three questions: * I am not sure which freesurfer ATLAS these values correspond to? Is there any way to tell from the name of structures? I have attached two text files including the header of the tables. * How can I visualize those values on the inflated brain? Something like this: http://pysurfer.github.io/examples/plot_parc_values.html This package is a great but unfortunately very unstable (at least on my laptop). It visualizes the brain but crashes immediately! No time to save the results. Is there any MATLAB equivalent? * What is the best way to visualize the values for the subcortical structures? Any comment is highly appreciated, Again, I am sorry if those are naive questions. Thanks,

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Catastrophic Surface Inaccuracies
by Jonathan Holt 28 Apr '14

28 Apr '14

Hi all, I would love information on how best to tackle and alleviate this type of surface issue. Images attached.

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Fw: Re: convert volume-based mni152 space into fsaverage surface space(MNI305)
by charujing123 28 Apr '14

28 Apr '14

Hi doug, Thanks doug. I cannot see my last e-mail file in the https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/index.html#35468. However I can receive it in my box, and none reply it. Maybe pitfalls in the network so that you cannot read my last e-mail file. So I send my last e-mail file to the freesurfer list again. Also I send to you. Looking forward to your new reply. Thanks again. All the best. Rujing Zha 2014-04-26 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-04-25 19:22 主题：Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) 收件人："Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Hi FS experts and users, Is there anyone can help me? Any reply will be highly appreaciated. Thanks. All the best. Rujing Zha 2014-04-25 charujing123 发件人："charujing123"<charujing123(a)163.com> 发送时间：2014-04-24 09:43 主题：Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) 收件人："Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Hi doug, Thanks doug. I used this DAT file,and the command termination without any problem.However the mask file dosenot overlay the rIPL area but frontal area when the mask file and fsaverage file were loaded in the freeview. Here are my scripts for creating the mask. mri_vol2surf --hemi rh --reg $FREESURFER_HOME/average/mni152.register.dat --mov ./rIPL.nii --o ./rIPL_mask.mgh --trgsubject fsaverage Source file volume-based mask ROI "rIPL.nii" is in the MNI152 space, and two snapshot can be got in the attachment. Also registrated surface ROI mask rIPL_mask.mgh snapshot can be got in the attachment. Here is its output in the command window. ========================================================================================= srcvol = ./rIPL.nii srcreg = /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume WARNING: the voxel resolution in the source volume (2,2,2) differs from that listed in the registration file (1,1,1) Reading surface /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 21146 Writing to ./rIPL_mask.mgh Dim: 163842 1 1 ================================================================================================= Thanks All the best Rujing Zha 2014-04-24 charujing123 发件人：Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2014-04-22 23:53 主题：Re: [Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305) 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： Use mri_vol2surf with $FREESURFER_HOME/average/mni152.register.dat On 04/21/2014 10:20 PM, charujing123 wrote: > Hi FS experts and users, > I created a mask volume, whose space is in MNI152 space. And I want to > convert this volume into surface-based in fsaverage. > How can I realize this? > Thanks > All the best. > Rujing Zha > 2014-04-22 > ------------------------------------------------------------------------ > charujing123 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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R: R: Re: labels of thalami
by stdp82＠virgilio.it 28 Apr '14

28 Apr '14

My apologies, but how can I visualize and check the labels obtained by mri_cor2label? Thanks, Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 28-apr-2014 19.23 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: labels of thalami Thank you very much!! ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 28-apr-2014 19.21 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] labels of thalami Use mri_cor2label On 04/28/2014 01:11 PM, stdp82(a)virgilio.it wrote: > Hi list, > > I'd like to obtained .labels of thalami to use it in FSL. > > How can I do it? > > Thanks, > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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R: Re: labels of thalami
by stdp82＠virgilio.it 28 Apr '14

28 Apr '14

Thank you very much!! ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 28-apr-2014 19.21 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] labels of thalami Use mri_cor2label On 04/28/2014 01:11 PM, stdp82(a)virgilio.it wrote: > Hi list, > > I'd like to obtained .labels of thalami to use it in FSL. > > How can I do it? > > Thanks, > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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R: labels of thalami
by stdp82＠virgilio.it 28 Apr '14

28 Apr '14

My apology. Here, the responce http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32645.html ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 28-apr-2014 19.11 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] labels of thalami Hi list, I'd like to obtained .labels of thalami to use it in FSL. How can I do it? Thanks, Stefano

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labels of thalami
by stdp82＠virgilio.it 28 Apr '14

28 Apr '14

Hi list, I'd like to obtained .labels of thalami to use it in FSL. How can I do it? Thanks, Stefano

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longitudinal recon-all -long error
by Corinna Bauer 28 Apr '14

28 Apr '14

Hello, I am on the recon-all -long step of the longitudinal processing stream and the final time point exits with errors at the mri_convert stage. mri_convert -at /home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta -odt uchar -rt cubic /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop.long.test_subject_template/mri/orig.mgz mghRead(/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz): could not read 262144 bytes at slice 4 I still have plenty of space left on the drive total used free shared buffers cached Mem: 16348132 14856524 1491608 0 534916 6193928 -/+ buffers/cache: 8127680 8220452 Swap: 16690172 573232 16116940 Any suggestions? The two previous timepoints finished without error. Corinna

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R: Re: ROI in FreeSurferColorLUT.txt
by stdp82＠virgilio.it 28 Apr '14

28 Apr '14

Thank you very much! A last question, please. Therefore, do you are working also on SLF I and SLF II implementation in TRACULA? If yes, how much time might be required to do it? (I'm writing a paper and I may wait these new tracts). Stefano ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 28-apr-2014 1.54 A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] ROI in FreeSurferColorLUT.txt Hi Stefano sorry, those are not ready yet, and the tracts do come from tracula Bruce On Mon, 28 Apr 2014, stdp82(a)virgilio.it wrote: > Hi list, > I'm noting these regions in FreeSurferColorLUT.txt. How can I obtained > structural information from them? > > 8001 Thalamus-Anterior 74 130 181 0 > 8002 Thalamus-Ventral-anterior 242 241 240 0 > 8003 Thalamus-Lateral-dorsal 206 65 78 0 > 8004 Thalamus-Lateral-posterior 120 21 133 0 > 8005 Thalamus-Ventral-lateral 195 61 246 0 > 8006 Thalamus-Ventral-posterior-medial 3 147 6 0 > 8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 > 8008 Thalamus-intralaminar 232 146 33 0 > 8009 Thalamus-centromedian 4 114 14 0 > 8010 Thalamus-mediodorsal 121 184 220 0 > 8011 Thalamus-medial 235 11 175 0 > 8012 Thalamus-pulvinar 12 46 250 0 > 8013 Thalamus-lateral-geniculate 203 182 143 0 > 8014 Thalamus-medial-geniculate 42 204 167 0 > > and from > > 6010 Left-SLF1 236 16 231 0 > > 6020 Right-SLF1 237 18 232 0 > > 6030 Left-SLF3 236 13 227 0 > 6040 Right-SLF3 236 17 228 0 > > 6050 Left-CST 1 255 1 0 > 6060 Right-CST 2 255 1 0 > > 6070 Left-SLF2 236 14 230 0 > 6080 Right-SLF2 237 14 230 0 > > Are the tracts different from tracts product by TRACULA? and can I use them > with TRACULA outputs? > > Thanks, > > Stefano > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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HBM Hackathon - please distribute widely !
by Satrajit Ghosh 27 Apr '14

27 Apr '14

The 2014 Hackathon<http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3606> registration is open<https://www.humanbrainmapping.org/i4a/ams/conference/conference.cfm?confere…>! This unique 3-day event (June 5-7) will be held prior to annual meeting of the Organization for Human Brain Mapping (OHBM)<http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3565>at the legendary c-base <http://c-base.org/>, a decked-out collaborative art and technology space at the heart of the Berlin hacker community. In keeping with the spirit of prior neuroimaging hackathons such as OHBM 2013<http://ohbm-seattle.github.io/>and Brainhack <http://www.brainhack.org/> 2012 and 2013<http://www.brainhack.org/>, participants will have the opportunity to propose collaborative projects and engage in a number of open challenges. For updated information on the developing Hackathon content, and to contribute your own ideas, check out www.brainhack.org. Current projects include the Sage Alzheimer’s Disease Challenge<https://www.synapse.org/#%21Synapse:syn2290704>, cloud computing tutorials with NITRC<https://aws.amazon.com/marketplace/pp/B00AW0MBLO> - <https://aws.amazon.com/marketplace/pp/B00AW0MBLO>CE<https://aws.amazon.com/marketplace/pp/B00AW0MBLO>and Amazon Web Services, workshops on data-sharing and meta-analysis, and many others initiated by scientists from the brain imaging community (see http:// <http://brainhack.org/categories/hackathon2014/>brainhack.org<http://brainhack.org/categories/hackathon2014/> /categories/hackathon2014/ <http://brainhack.org/categories/hackathon2014/>). Participants engaged in the Alzheimer’s Disease Challenge will have the unique opportunity to set an initial benchmark for a multi-phase effort to identify early accurate predictive biomarkers that can inform the scientific, industrial and regulatory communities about the disease. Join this vibrant community and help build open neuroscience initiatives in one of the most unique tech venues in Berlin. To keep the collaborations flowing, meals and refreshments are all included in the registration costs and will be provided on-site, as well as $100+ in Amazon Web Service credits for your computational needs. Participation is limited, so we encourage you to register now<https://www.humanbrainmapping.org/i4a/ams/conference/conference.cfm?confere…>. The spirit of the Hackathon will also be continuing into the OHBM meeting in Hamburg from June 8-12, where a collaboration space will be available in the conference venue. This space will be open to all OHBM attendees to discuss, present, and continue working on hackathon projects. OHBM Hackathon website: https://www.humanbrainmapping.org/hackathon Registration: https://www.humanbrainmapping.org/i4a/ams/conference/conference.cfm?confere… Projects: http://www.brainhack.org/

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