Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

rh or lh?
by Yang, Daniel 02 Oct '13

02 Oct '13

Dear FreeSurfer Experts, Is there a program that can automatically judge whether a mgh is in the rh or lh? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

2 2

UPDATES on Brainhack 2013 (including stipend application extension)
by MCLAREN, Donald 01 Oct '13

01 Oct '13

Dear All, Brainhack 2013 will be taking place in just under a month outside of Paris, France. A welcome reception will be held on the evening of October 23rd to be followed by the hackathon on October 24th, 25th, and 26th. Brainhack 2013 will be highlighted by "Ignite" talks by: - *Yves Burnod, PhD,<http://www.imed.jussieu.fr/en/outils/affiche_personne.php?pers_id=217> INSERM (French national Institute for Health)* - *Jean Daunizeau, PhD,<https://sites.google.com/site/jeandaunizeauswebsite/>l’Institut du Cerveau et de la Moelle épinière* - *Martin Lindquist, PhD, <http://www.biostat.jhsph.edu/~mlindqui/> Department of Biostatistics of the Johns Hopkins University Bloomberg School of Public Health.* - *Ziad Saad, PhD,<http://intramural.nimh.nih.gov/research/clinicians/sc_saad_z.html> US National Institutes of Mental Health Statistical and Scientific Computing Core* - *Gaël Varoquaux, PhD, <http://gael-varoquaux.info/> INRIA at the Neurospin* - *Xinian Zuo, PhD, <http://lfcd.psych.ac.cn/> Institute of Psychology, Chinese Academy of Science* UPDATES: We have four important updates about Brainhack 2013: (1) Brainhack.org back online after being offline at the end of last week and over the weekend. Details about Brainhack 2013 can now be found there. (2) Due to the technical problems last week, we've extend the stipend application deadline to 11:59 PM EST on Thursday October 3rd. See brainhack.org for details on how to apply. (3) Attendees can now complete their registration by paying the registration fees at: http://dr01.azur-colloque.cnrs.fr Instructions on this process can be found here: http://www.brainhack.org/?page_id=5425. The deadline for registering is October 15th and payment must be received by October 16th. (4) If you want to have your poster abstract appear in the Brainhack 2013 Program, please submit your abstract online at brainhack.org. Posters will be presented electronically during the welcome reception. Hope to see you next Month. > Please let Donald McLaren know if you have any questions. He can be > reached via email: mclaren.donald(a)gmail.com >

1 0

Re: [Freesurfer] MNI152 to 305 conversion
by Douglas N Greve 01 Oct '13

01 Oct '13

View it in tkmedit to see if it is really a problem with your vol2vol command. doug On 09/30/2013 07:33 PM, Paul Beach wrote: > No. That was just a general example of how the image looks - from a > stock google image of an FSL brain (I'm not in the lab and so cannot > put up actual images). I've been using AFNI to view them. > > > On Mon, Sep 30, 2013 at 7:23 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Is this in tkmedit? > > > On 09/30/2013 06:59 PM, Paul Beach wrote: > > Hi Doug, > > Sorry, I should have been more specific. I meant for when one > looks at the resulting transformation in a sagittal view. > > More specifically... > Instead of this: > Inline image 1 > > It looks more like this (though more like a 70degree shift > than 90): > Inline image 2 > The other views are obviously affected as well. Performing a > dataset "nudge" using afni generally "corrects" this problem, > but I'd like to prevent it from happening in the first place. > > I'm suspicious that this is occurring because I'm using > '/mni305.cor.mgz/' instead of '/mni305.2mm.nii.gz/' for the > 'mov' command. However, I don't have the latter file anywhere > in my Freesurfer directory. The former file is the closest > thing I could find. > > > Thoughts? > Paul > > > > On Mon, Sep 30, 2013 at 5:52 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > what do you mean the frontal lobe is pointing straight up? > > > > > On 09/30/2013 02:32 PM, Paul Beach wrote: > > Freesurfer experts, > > > > I'm attempting to utilize an archived e-mail's contents > to resample > > data in MNI152 to 305. > > > > The script I'm using is as follows: > > /mri_vol2vol \/ > > /--mov > > > > /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz > > \/ > > /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \/ > > /--reg > > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ > > /--inv --o FSL_MNI305_2mm.nii.gz/ > > / > > / > > / > > / > > This series of commands is based on the following suggestion > from Doug > > in a previously archived e-mail exchange from someone > attempting > to do > > something similar: > > />> To go from mni152 to the MNI305 2mm space, use/ > > />>/ > > />> mri_vol2vol --mov mni305.2mm.nii.gz \/ > > />> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \/ > > />> --reg > > > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ > > />> --inv --o output.mni305.2mm.nii.gz/ > > />>/ > > />> This will resample MNI152_T1_2mm.nii.gz (or anything > in that > > space) to the/ > > />> mni305 2mm space./ > > > > > > However, this changing the orientation of my data - > essentially all > > images are being rotated 90degrees so the frontal lobe > is pointed > > straight up. > > > > Are there any suggestions to ameliorate this problem? > > > > Thanks! > > -- > > Paul Beach > > DO/PhD candidate - Year VI > > Michigan State University > > - College of Osteopathic Medicine > > - Neuroscience Program > > - Bozoki Lab: Neurology/Radiology > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <http://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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: 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/ > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology -- 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/

3 15

Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview
by Douglas N Greve 01 Oct '13

01 Oct '13

I thinkyou just need to change the aparc to be either transparent or outline. On 10/01/2013 07:44 PM, Yang, Daniel wrote: > Hi Doug, > > I think I find out where the problem is. Actually the mri_vol2surf > works nicely (and it's also true that tksurfer with -mni152reg samples > the overlay to the white surface by default instead of to the pial > surface.) > > The problem is in freeview + rh.aparc.annot. > > If you do the following for the attached rh mgh file, you will see it > correctly displayed: > > tksurfer fsaverage rh inflated -overlay rh.pial_surface.mni305.mgh > > If you overlay this mgh in freeview with rh.inflated surface, but > without loading rh.aparc.annot, it also displays correctly. > > However, once I load the rh.aparc.annot, I see something like attached > png. > > Thanks! > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > On 10/1/13 6:11 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > I don't understand what you mean by a "much smaller brain". Can you > elaborate? > On 10/01/2013 06:10 PM, Yang, Daniel wrote: > > Hi Doug, > > I understand. But the end product turned out to be a much smaller > brain … so I thought there is something wrong. What should I > do here? > > Thanks! > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > On 10/1/13 6:00 PM, "Douglas N Greve" > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu%3E>> wrote: > > > The way the software is set up, you should use > mni152.register.dat > with > mri_vol2surf to map mni152 volumes to the fsaverage (ie > MNI305) > surfaces > > doug > > > On 10/01/2013 05:49 PM, Yang, Daniel wrote: > > Hi Doug, > > Just checking again, because I haven't heard from > you. So the > purpose > is to use mri_vol2surf is convert MNI152 to a FreeSurfer > (MNI305) mgh > file. I am not sure about the correct register.dat to > use. The > mni152.register.dat is for MNI305 -> MNI152 though. > > I'm assuming that there exists some sort of inverse > mni152.register.dat somewhere? > > Thanks! > Daniel > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > On 9/27/13 6:44 AM, "Yang, Daniel" > <yung-jui.yang(a)yale.edu <mailto:yung-jui.yang@yale.edu> > <mailto:yung-jui.yang@yale.edu> > <mailto:yung-jui.yang@yale.edu> > <mailto:yung-jui.yang@yale.edu%3E> > <mailto:yung-jui.yang@yale.edu%3E%3E>> wrote: > > Thanks Doug! > > Because it maps from a MNI152 space to the > FreeSurfer average > space, do you know what register.dat I can use? > > Is it some sort of inverse mni152.register.dat? > Thanks! > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > On 9/26/13 12:26 PM, "Douglas N Greve" > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu%3E> > <mailto:greve@nmr.mgh.harvard.edu%3E%3E>> wrote: > > They might be sampling to different > surfaces. To make > sure > they show the > same exact thing, try mapping the data to > the surface > with > mri_vol2surf > doug > On 09/25/2013 08:31 AM, Yang, Daniel wrote: > > Dear FreeSurfer Experts, > > I am trying to visualize fMRI activation > (generated from > fsl) on the > fsaverage inflated surface, using > mni152.register.dat. > > It's odd that I find the results to be > slightly > different > between > tksurfer and freeview. However, I made > sure that I am > using the same > threshold... > > Judging from fslview, I think the result > with > freeview is > more > accurate -- is it due to tksurfer > loading orig.mgz by > default, and > free view loading something else? > > Thanks! > Daniel > > -- > Yung-Jui "Daniel" Yang, PhD > Postdoctoral Researcher > Yale Child Study Center > New Haven, CT > (203) 737-5454 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@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 > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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/ > > -- 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/

2 1

overlay mni152 activation -- difference between tksurfer and freeview
by Yang, Daniel 01 Oct '13

01 Oct '13

Dear FreeSurfer Experts, I am trying to visualize fMRI activation (generated from fsl) on the fsaverage inflated surface, using mni152.register.dat. It's odd that I find the results to be slightly different between tksurfer and freeview. However, I made sure that I am using the same threshold... Judging from fslview, I think the result with freeview is more accurate -- is it due to tksurfer loading orig.mgz by default, and free view loading something else? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

2 7

DODS slope information
by Jacobs H (NP) 01 Oct '13

01 Oct '13

Hi Freesurfers, I just looked at my cortical thickness results, in which I performed an interaction between group (2 groups) and cognition (continuous). I see regions popping up, which is great! Especially since they are related to the task. Now, I made a scatterplot of some of these vertices to get a better understanding of the effect. However, I am wondering how I can figure out if the slope within each group is significant. How can I examine that? Thanks! Heidi ================================================ Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jacobs(a)maastrichtuniversity.nl www.maastrichtuniversity.nl www.heidijacobs.nl Dr. Tanslaan 12, 6229 ET Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 38 84 090 F +31 43 38 84 092 ================================================

2 1

Xhemi-Fsaverage Vs myatlas
by amirhossein manzouri 01 Oct '13

01 Oct '13

Dear FS experts, I want to perform asymmetry study in a group of subjects. I have created myatlas.i3 from my data(86) based on the procedure from Xhemi page and tksurfer lh inflated of both fsaverage and myatlas image is attached! it has shown that my atlas is smaller in general and larger in temporal lobe! I wonder if this is correct and I can proceed to compare left and right Hemispheres? -- Best regards, Amirhossein Manzouri

2 1

co-registration: SWI images with FLAIR
by Ayaz, Muhammad 01 Oct '13

01 Oct '13

Dear All, Can I co-register SWI with FLAIR images using Freesurfer? thanks Ayaz The information contained in this message and any attachments is intended only for the use of 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 you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

2 1

Re: [Freesurfer] Transparency surface
by Arnaud Boré 01 Oct '13

01 Oct '13

Hi, Is there a way to see both side of the activation with a brain which looks like the pial ? Without inflated maybe I'm not really familiar with tksurfer. So far I used tksurfer fsaverage6 lh inflated by default. Thank you. Arnaud 2013/10/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Arnaud > > can you in general cc the list on these questions so that others can > answer. > > What you are trying to do is what the inflated surface is designed for. I > don't think the transparency thing would work - it would just be confusing > > > cheers > Bruce > > > On Tue, 1 Oct 2013, Arnaud Boré wrote: > > Hi Bruce, >> I added two pictures so you can see what I referred to. >> When I display the main surface, I'm able to see my activation. But when >> using the pial >> surface, it's hard to see the activation. I thought that if I could >> change the transparency of >> the surface, I will be able to see the other side (i.e., hidden in the >> sulci) of the >> activation (as shown in the main surface). >> >> Thank you for your answer. >> >> Arnaud >> >> >> >> 2013/10/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Arnaud >> >> why would transparency help? You should be able to view the overlay >> on any surface >> without transparency (the overlay defines the colors displayed on >> the surface). >> Can you explain further why the normal display in tksurfer doesn't >> do what you >> want? >> >> cheers >> >> Bruce >> >> On Tue, 1 Oct 2013, Arnaud Boré wrote: >> >> Dear Freesurfer experts, >> Using tksurfer I open an inflated surface and I display the >> pial >> surface. >> Then I load an overlay but I'm not able to see it correctly. >> Is it >> possible >> to put a transparency/opacity value for the surface so I can >> see >> better my >> overlay ? >> >> Thank you for your help >> >> Arnaud Bore >> >> >> >> >> >> 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<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. >> >> >> >> >> -- >> Arnaud BORE >> Research assistant >> Cellulaire : (001) 514-647-8649 >> >> >> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649

1 0

Re: [Freesurfer] Question about preproc-sess -no-subcort-mask
by Leila Reddy 01 Oct '13

01 Oct '13

Hi Doug, I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis). I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask. Thanks again, Leila Machine 1: --------------------------------------------------------------------- FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Kernel info: Darwin 10.8.0 i386 --------------------------------------------------------------------- Machine 2: --------------------------------------------------------------------- FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 --------------------------------------------------------------------- ________________________________ Date: Mon, 30 Sep 2013 17:48:15 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5249F19F.3070503(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed They do have the same default. Note that if you run preproc-sess with -no-subcort-mask and then run it again without -no-subcort-mask it will not generate a new file. Could that have happened? doug

2 4

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2013