Freesurfer

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30135 discussions

hippocampus question
by Jasmin Alves 09 Aug '16

09 Aug '16

Dear Freesurfer, I have noticed that the subcortical grey matter volume output for the hippocampus differs slightly from other segmentation methods, I was wondering if this is due to what subfields of the hippocampus are included in the segmentation. I was curious which subfields Freesurfer includes as regional boundaries for the hippocampus. Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Average Hippocampal Subfield Maps
by Jessica Sevick 09 Aug '16

09 Aug '16

Hello, I am wondering if it is possible to make average .mgz for the hippocampal subfields for a set of control images? Thanks, Jessica Sevick T: 403.944.8652 C: 587.576.6666

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Linking surface and volume coordinates in Freeview
by Isabelle Deschamps 09 Aug '16

09 Aug '16

Dear Freesurfer experts, In May 2016, one of the high priority on the Freeview Development board was to "Link the surfaces together (i.e. when you click on a vertex in the inflated surface, it should go to that vertex on the white and pial) & show identical vertex information in the Voxel Info panel. When clicking on a point on the 2D surface, automatically move the cursor in the 3D view to the closest point on the surface to that point in the volume." I couldn't find any information about whether this priority has been addressed yet or not. Would it be possible to have an update? Thank you in advance for the information, Isabelle

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Re: [Freesurfer] resample structural ROI in functional space?
by Kami Koldewyn 09 Aug '16

09 Aug '16

Never mind - for some inexplicable reason, I did not consider using mri_convert, which works splendidly for doing this. Sorry for posting when tired and before thoroughly exploring my options. -kami From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Kami Koldewyn <k.koldewyn(a)bangor.ac.uk<mailto:k.koldewyn@bangor.ac.uk>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, 8 August 2016 19:33 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] resample structural ROI in functional space? Hi All, I have a set of ROIs that were created in structural space, currently saved as volume masks. I would like to transform these into functional space, re-sampled to the functional resolution. Can anyone suggest a good way to do this? -kami Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office. Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office.

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 08 Aug '16

08 Aug '16

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Re: [Freesurfer] How does Optseq2 arrange order of conditions?
by 連志浩 06 Aug '16

06 Aug '16

Dear Douglas, I'm sorry that I didn't include previous correspondence in my email, from now on, I'll remember to include it. (I'm a new user of the FreeSurfer Mail Archive, I hope I include previous correspondence at this time.) Thanks for your reminding. Best Regards, Chih-Hao ________________________________ Date: Fri, 5 Aug 2016 11:45:55 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] How does Optseq2 arrange order of conditions? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <57A4B4B3.1000601(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed Please remember to include previous correspondence in your email. On 08/01/2016 04:22 AM, ? ?? wrote: > > Dear Douglas, > > Thanks for your explanation. These information are helpful to me. > > >I'm not sure what you mean. How can it be a delay if it is after > thetrial is over? > > I?m sorry for I didn?t describe my second question well. I think I can > take another situation to describe my question. > > If I have a experiment that present stimulus until participants > response, and I know the average RT of this experiment is 1500 ms > after pilot test. > > In this situation, should I +/- the duration of jitter/null condition > in terms of the duration of each stimulus? > > For example, if a part of sequence Optseq2 output is ? Con1 Null(500 > ms) Con2 Null(1500 ms)?, and one of participants takes 1000 ms to > response for Con1. > > Should I add 500 ms to the first Null? or I don?t need to anything? > > Thanks for your reading. > > Best Regards, > > Chih-Hao > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Freesurfer Info Page - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives. A searchable archive which of messages PRIOR to March 2004 is at ... -- 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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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internal capsule freesurfer
by 张献昌 06 Aug '16

06 Aug '16

Dear freesurfer developer, Hi, We recently processed some T1 data using Freesurfer .We want to extract internal capsule as roi. We found it appear in the ColorTableLUT as regions 155-158, but do not actually appear in any of the output parcellations.There is a message that Doug wrote some tools to do this in <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-October/020985.…>. I would appreciate it if anyone can send me the script intcapseg and it would be better if there is a file describing how to use it. Thanks!! Best Regards!

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September FreeSurfer Course in Boston Registration open
by Allison Moreau 05 Aug '16

05 Aug '16

The FreeSurfer group is offering a four-day FreeSurfer Tutorial and Workshop September 26th to 29th, 2016 at the Martinos Center in Charlestown, MA. You can register for the course on our course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an email confirmation that you successfully secured a seat in the course. *NOTE- We will hold the course even if 40 students are not registered, so you can make travel arrangements once you have received an email confirmation. -- Allison Moreau Research Technologist Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital

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Problems with QDEC
by Vikas Bandalli 05 Aug '16

05 Aug '16

Dear Freesurfers, Sorry if the question sounds too basic. 1. I am running an analysis on qdec with paired groups - normal and patients, To control for IntraCranialVolume(ICV),I am adding it as an 'nuisance factor',Is it correct? The suggested mode to add ICV to the tabled was to *demean* the ICV. But when I subtract the mean values from individual subject ICV values,I noticed that some of the subjects have a negative demeaned ICV value. My question is - How should I proceed to include the data,ignore the negative sign(because I thought a negative ICV makes no sense) and just keep the values or retain the numbers with the sign. Please correct me if I am going wrong in any of the steps. However,I ran two analysis - one with the sign retained and other with sign removed ,I noticed that both have very different results. 2. If I want to see the effect due to lithium within the patient group (Between patients with and without psychosis) how should I design the matrix in GUI. I designed the following format Fixed factor :- Diagnosis - Psychotic-pt Non-Psychotic-pt Co-variate :- Lithium use :- 1 - lithium user 0 - non user Nuisance factor :- ICV Is this design correct? If not how should I construct it ? Also what query would contain the result for anticipated question My intention is to control for Diagnosis and then see effect/change due to lithium use. Thank you very much -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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Re: [Freesurfer] Freesurfer Digest, Vol 150, Issue 6
by Caroline Beelen 05 Aug '16

05 Aug '16

My command line is: mris_label2annot --subject fsaverage --hemi lh --ctab aparc.annot.ctab --annot myaparc --l lh.fusiform.label --l lh.inferiorparietal.label (etc.) --nhits nhits.mgh (I have version 5.3) Regards, Caroline Message: 3 Date: Wed, 3 Aug 2016 09:30:48 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mapping error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <f3f77469-16ad-6fdf-f647-80aee162dbfc(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" what is your command line? On 8/3/16 6:00 AM, Caroline Beelen wrote: > > Dear FS, > > An aparc.annot ctab file was created but I got the following error: > > Colortable:aparc.annot.ctab > > Annotname: myaparc > > Nhitsfile nhits.mgh > > Nlabels 6 > > Labeltresh 0 0.00000 > > Loading freesurfer/fsaverage/surf/lh.orig > > 1 -1 not found > > 2 -1 not found > > 3 -1 not found > > Etc? > > Mapping unhit to unknown > > Found 132101 unhit vertices > > Writing annot to freesurfer/fsaverage/lh.myaparc.annot > > I guess my ctab file is incorrect? I included an example of a label > with it. > > Thanks again for your help. > > Caroline > > -----Oorspronkelijk bericht----- Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens freesurfer-request(a)nmr.mgh.harvard.edu Verzonden: woensdag 3 augustus 2016 18:00 Aan: freesurfer(a)nmr.mgh.harvard.edu Onderwerp: Freesurfer Digest, Vol 150, Issue 6 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/listinfo/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. Re: brain mask and T1 are not the same size (Isabelle Deschamps) 2. Re: Coordinates in TRACULA group analysis (Anri WATANABE) 3. Re: mapping error (Douglas Greve) 4. Re: Multiple Comparison Question for surface-based analyses (Douglas Greve) 5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki) 6. Re: brain mask and T1 are not the same size (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 3 Aug 2016 10:50:30 +0000 From: Isabelle Deschamps <isabelle.deschamps.1(a)ulaval.ca> Subject: Re: [Freesurfer] brain mask and T1 are not the same size To: "<freesurfer(a)nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <8F31A8F6-59C6-4D12-A2A4-2EF526465775(a)ulaval.ca> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20160803/f… ------------------------------ Message: 2 Date: Wed, 3 Aug 2016 20:19:09 +0900 From: Anri WATANABE <z2aanri(a)koto.kpu-m.ac.jp> Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAAw-JJEAwC33OaX6oaMeuEcT3q06Ah8ZYfD6NuuO32bn-eHgNA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Anastasia, Thank you for your kind explanation. I can be understanding how TRACULA tracts white matter pathways. At each position (in training subjects, not in new subjects of my data) probability that next goes for which direction to every labels in the aparc+aseg (not with setting a certain ROI) is computed with use of training subjects. The prior probabilities are made from training subjects (your publication in 2011) and they are based on manual labeling (the manual labeling tracts are referred to Wakana et al. 2007). Then when white matter pathways are reconstructed in my subjects, TRACULA computes anatomical priors in each subjects in my data in pre-processing and probability distributions from anatomical priors and by fitting ball-and-stick model. Is this comprehension ok? Best Regards, Anri ********************************************************************** ???????????? ???????? ?? ?? ********************************************************************** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ********************************************************************** 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu>: > > Hi Anri - Instead of hard-coding some ROIs in the white matter that the > tract is forced to go through, TRACULA uses information like "what is the > probability that this tract goes lateral/anterior/etc to XXX", where XXX > any of the labels in the aparc+aseg. TRACULA computes these prior > probabilities from a set of training subjects, where the tracts have been > labeled manually. So it knows how likely a tract is to go through a certain > aparc+aseg label, or to he left, right, anterior, etc of a certain > aparc+aseg label. This is computed separately at each position along the > tract. It's computed from the training subjects, and then used when > reconstructing the tract in the new subject that you run TRACULA on. > > Hope this helps, > a.y > > On Sun, 31 Jul 2016, Anri WATANABE wrote: > > Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if >> ROIs are not >> >> set how determine the origin and the end of a certain tract? I think that >> the first we >> have to determine the origin and the end of the tract, the second it >> constructs possible >> pathway not with the deterministic way (only 1 direction / 1 voxel) but >> with the >> probabilistic way (considering which direction should be next to). Is >> this comprehension >> wrong? >> Thank you. >> >> Anri >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> ********************************************************************** >> >> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki < >> ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri - TRACULA does not use deterministic ROIs. It uses a >> probabilistic >> model of how likely each tract is to go through or next to each of >> the labels >> of the freesurfer subcortical segmentation and cortical >> parcellation, as a >> function of position along the trajectory of the tract. >> >> Best, >> a.y >> >> On Sun, 31 Jul 2016, Anri WATANABE wrote: >> >> Hi Anastasia, >> Thank you! It seems work well!! >> I have another question. Are ROIs for automatic tractography >> in >> TRACULA the same ROIs >> presented in Wakana et al. 2007? >> >> Anri >> >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> >> ********************************************************************** >> >> 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri - The problem is in this line: >> >> set cmd = ($cmd --ref $cvstempdir/$cvstemp) >> >> It should be changed to this: >> >> set cmd = ($cmd --ref >> $cvstempdir/$cvstemp/mri/norm.mgz) >> >> For this to take effect, you need to run "which >> trac-all" >> and make the change in >> the trac-all file that the which commands shows you. >> >> Hope this helps, >> >> a.y >> >> On Fri, 15 Jul 2016, Anri WATANABE wrote: >> >> Hi, AnastasiaThis is trac-all.local-copy from 1 >> subject. Thank you! >> >> Anri >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University >> of >> Medicine >> >> >> ********************************************************************** >> >> 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri - This may be a bug that was fixed >> at >> some point. Can >> you send me the scripts/trac-all.local-copy >> from >> one of your >> subjects? Thanks! >> >> a.y >> >> On Mon, 11 Jul 2016, Anri WATANABE wrote: >> >> Hi Anastasia,There is an error in .log >> files of left >> corticospinal tract in cvs template >> and I >> attached >> one >> of file. In addition .log files of >> right >> corticospinal tract in cvs template >> doesn't exist. >> Thanks in advance. >> >> Anri >> >> >> >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural >> University of >> Medicine >> >> >> >> ********************************************************************** >> >> 2016-07-07 20:12 GMT+09:00 Anastasia >> Yendiki >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri - Is there an error in >> the >> stats/*.log >> files for the different tracts? >> >> a.y >> >> On Tue, 5 Jul 2016, Anri >> WATANABE >> wrote: >> >> Dear Anastasia, >> >> I use TRACULA to obtain >> diffusion >> measures at each voxel in a certain >> pathway for >> group analysis, but >> there aren't >> stats/*.path.mean.txt >> files. I found .log files >> >> (<tract>_PP.avg33_mni_bbr.log) >> which >> exist >> 1 file per 1 tract, except >> corticospinal >> tract which has 2 .log files. >> >> Command: trac-all ?stat ?c >> >> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >> >> Error log: Loading output >> reference >> volume from >> >> >> /Applications/freesurfer/subjects/cvs_avg35 >> >> corRead(): can't open file >> >> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >> >> ERROR: Could not read >> >> /Applications/freesurfer/subjects/cvs_avg35 >> >> >> I attached dmrirc.example >> (configuration >> file) and >> <subjd>/scripts/trac-all.log. >> >> >> Thanks in advance, >> Anri >> >> >> >> >> >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto >> Prefectural >> University of Medicine >> >> >> >> >> ********************************************************************** >> >> 2016-06-03 9:51 GMT+09:00 >> Anri >> WATANABE >> <z2aanri(a)koto.kpu-m.ac.jp>: >> Hi, Anastasia. >> There aren't any .log >> files >> but text >> files like >> lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. >> I guess text >> files complete all >> pathways >> and >> measures. >> >> >> >> >> >> ********************************************************************** >> ???????????? >> ???????? >> ?? ?? >> >> >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto >> Prefectural >> University of Medicine >> >> >> >> >> ********************************************************************** >> >> 2016-06-02 3:03 GMT+09:00 >> Anastasia >> Yendiki <ayendiki(a)nmr.mgh.harvard.edu >> >: >> >> Thanks, Anri. So the >> previous >> steps seem to have run fine. Are >> there any >> .log >> files >> created in the >> stats/ >> folder, >> which is created by trac-all -stat? >> >> On Wed, 1 Jun 2016, >> Anri >> WATANABE >> wrote: >> >> Hi >> Anastasia, This >> is a >> <subjid>/scripts/trac-all.log of one >> subject of >> the group. >> >> Thanks, >> Anri >> >> >> >> >> >> ********************************************************************** >> >> ???????????? >> ???????? >> ?? ?? >> >> >> >> >> ********************************************************************** >> Anri WATANABE, >> M.D. >> Department of >> Psychiatry, >> University >> Hospital, Kyoto >> Prefectural University of Medicine >> >> >> >> >> ********************************************************************** >> >> 2016-05-31 >> 22:55 >> GMT+09:00 >> Anastasia Yendiki >> >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> Hi Anri >> - >> Can you also >> send your log file >> (scripts/trac-all.log)? >> I'll need to >> see >> what >> exactly >> was >> running >> when the error occurred. Thanks! >> >> a.y >> >> On Sat, >> 28 >> May 2016, >> Anri WATANABE wrote: >> >> >> Hello >> Anastasia,sorry for few information >> and >> let me tell >> you >> command and >> >> error >> log. >> >> Command: trac-all ?stat ?c >> >> >> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >> >> >> Error >> log: Loading output reference volume >> from >> >> >> /Applications/freesurfer/subjects/cvs_avg35 >> >> >> corRead(): can't >> open file >> >> >> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >> >> >> ERROR: >> Could not >> read >> >> >> /Applications/freesurfer/subjects/cvs_avg35 >> >> >> >> dmrirc.example (configuration file) is >> attached to >> this >> e-mail. >> >> >> Thanks >> in >> advance, >> >> Anri >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> ???????????? >> >> ???????? >> ?? >> ?? >> >> >> >> >> >> ********************************************************************** >> >> Anri >> WATANABE, >> M.D. >> >> Department of >> Psychiatry, >> >> University >> Hospital, Kyoto Prefectural >> University of >> Medicine >> >> >> >> >> >> ********************************************************************** >> >> >> 2016-05-27 22:57 >> GMT+09:00 Anastasia Yendiki >> >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> >> >> Hi Anri - >> I do not know what command line you >> ran >> and >> what your >> >> configuration >> file looks like, so it is very >> >> >> hard for >> me to suggest solutions. >> >> >> >> Best, >> >> >> a.y >> >> >> >> On Fri, 27 >> May 2016, Anri WATANABE wrote: >> >> >> >> Hi >> Anastasia, >> >> >> >> Thank you for your answer. >> >> >> >> There aren't stats/*.path.mean.txt >> files and >> terminal says >> 'Could >> >> not >> read >> >> >> >> >> /Applications/freesurfer/subjects/cvs_avg35.' I >> >> >> >> checked >> >> >> /Application/freesurfer/subjects/cvs_avg35 >> folder >> and >> >> couldn't find >> COR-.info file. >> >> >> >> Could you tell me any resolutions, >> please? >> >> >> >> >> Thanks, >> >> >> Anri >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> ???????????? >> >> >> >> ???????? >> >> >> ?? >> ?? >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> Anri >> WATANABE, M.D. >> >> >> >> Department of Psychiatry, >> >> >> >> University Hospital, Kyoto Prefectural >> University >> of Medicine >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> >> 2016-05-21 6:48 GMT+09:00 Anastasia >> Yendiki >> >> <ayendiki(a)nmr.mgh.harvard.edu>: >> >> >> >> >> Hi Anri - The FA values are >> extracted in >> the native >> space >> of >> each subject, >> which is why >> >> >> >> those are the only >> >> >> >> coordinates that you see. If you >> want to >> display the >> >> results of your >> analysis on an average >> >> >> >> path, after >> >> >> >> running trac-all -stat, you can use >> the >> >> stats/*.path.mean.txt files (see also >> the >> last part >> >> >> of >> the TRACULA >> >> >> >> tutorial). >> >> >> >> >> Best, >> >> >> >> a.y >> >> >> >> >> On Wed, 18 May 2016, Anri WATANABE >> wrote: >> >> >> >> >> Dear experts, >> >> >> >> I use TRACULA to examine a >> measure >> (FA) at each >> voxel >> >> in one >> pathway. >> >> >> >> pathstats.byvoxel.txt files >> show >> coordinates in >> >> native >> space and >> after converting >> >> >> >> those the new >> >> >> >> files don't show any >> coordinates >> which are in >> MNI >> >> space. >> >> >> >> Could you tell me how can I >> know >> MNI >> coordinate >> >> values? >> >> >> >> >> Thank you! >> >> >> >> >> >> Regards, >> >> >> >> Anri >> >> >> >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> ???????????? >> >> >> >> ???????? >> >> >> >> ?? ?? >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> Anri WATANABE, M.D. >> >> >> >> Department of Psychiatry, >> >> >> >> University Hospital, Kyoto >> Prefectural >> University of >> >> Medicine >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> 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. >> >> >> >> >> >> >> _______________________________________________ >> >> 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 >> >> > ... > > [???????????] > _______________________________________________ > 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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