[Freesurfer] Unsupported slice timing problem
We recently ran into an issue with Freesurfer's mri_convert tool where it gives an error of "unsupported slice timing pattern". We have some NIFTI MPRAGE files that have a "slice_code" with a value of NIFTI_SLICE_ALT_INC2 (=5). Issue arises in utils/mriio.c (line 9549 of rev:stable5), two slice_code possibilities are not included in the if-statement, NIFTI_SLICE_ALT_INC2 and NIFTI_SLICE_ALT_DEC2. These are defined in include/nifti1.h (comment says they were added in 2005), so I'm checking to see if there is a reason they are not allowed, or if this bit of code was just never updated to reflect the latest nifti1.h. Thanks for any help, -Louie Perkins ___ 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.
Re: [Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
Hello Bruce, Thank you for your reply. I used recon-all -make all -s subject. Thanks, Jeff On Thu, Jun 16, 2011 at 3:11 PM, Bruce Fischl wrote: > Hi Jeff > > what command did you run to run them over? > > cheers > Bruce > > On Thu, 16 Jun 2011, Jeff Sadino wrote: > > Hello, >> >> When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects >> Directory, and then reran them using the FS5 recon-all stream. This >> updated >> their subject folders with the FS5 changes, but not in as many places as I >> would have thought. For example, on 6 test subjects, I created their FS5 >> folders from FS4 folders that I copied over and then ran the FS5 recon-all >> stream. I also created another copy of their FS5 folders from scratch. >> The >> average difference in their ICV values was -12,000 mm^3. Is it to be >> expected that FS5 reconstructions running on FS4 folders will not include >> all possible improvements? If I want to get an accurate an ICV >> measurement >> as possible, is it advisable to rerun all of my subjects in FS5, starting >> from scratch? >> >> As always, thank you for your valuable assistance! >> Jeff Sadino >> >> > > 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.
Re: [Freesurfer] interpolation during conform step of oblique acquisitions
Hi Mike, the intent was to be independent of the prescription of the slices so that we could always depend on voxel coordinates having some anatomical meaning, regardless of what crazy slice orientation was prescribed. Not sure if Doug has some easier work around for you to prevent the rotation. cheers Bruce On Thu, 16 Jun 2011, Michael Harms wrote: > > Hi guys, > > I'm curious why the conform step of mri_convert (in generating > mri/orig.mgz) automatically interpolates oblique acquisitions. Is this > a historical legacy? Something mandated by other elements of the FS > pipeline? As a consequence of this behavior, if you have an oblique > acquisition that was intentionally aligned to the actual anatomy of a > given subject's brain (e.g., using AutoAlign to generate a AC-PC aligned > acquisition), unless one manually alters the qform in the input NIFTI > file to remove the "oblique" components of the xform, there will be an > interpolation in the generation of the mri/orig.mgz, which brings with > it blurring (i.e., the same sort of concerns that prompt one to use a > single MPRAGE, rather than the average of two MPRAGEs) > > Just curious... > > thanks, > -MH > > > ___ 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.
Re: [Freesurfer] Name of the atlas
it's the version of Christophe Destrieux's atlas he updated in 2009 cheers Bruce On Thu, 16 Jun 2011, Dalwani, Manish wrote: > What atlas does aparc2009 represent? > > Regards, > Manish Dalwani > Sr. PRA > Dept. of Psychiatry > University of Colorado > ___ 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.
Re: [Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
Hi Jeff what command did you run to run them over? cheers Bruce On Thu, 16 Jun 2011, Jeff Sadino wrote: > Hello, > > When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects > Directory, and then reran them using the FS5 recon-all stream. This updated > their subject folders with the FS5 changes, but not in as many places as I > would have thought. For example, on 6 test subjects, I created their FS5 > folders from FS4 folders that I copied over and then ran the FS5 recon-all > stream. I also created another copy of their FS5 folders from scratch. The > average difference in their ICV values was -12,000 mm^3. Is it to be > expected that FS5 reconstructions running on FS4 folders will not include > all possible improvements? If I want to get an accurate an ICV measurement > as possible, is it advisable to rerun all of my subjects in FS5, starting > from scratch? > > As always, thank you for your valuable assistance! > Jeff Sadino > ___ 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] Name of the atlas
What atlas does aparc2009 represent? Regards, Manish Dalwani Sr. PRA Dept. of Psychiatry University of Colorado ___ 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] interpolation during conform step of oblique acquisitions
Hi guys, I'm curious why the conform step of mri_convert (in generating mri/orig.mgz) automatically interpolates oblique acquisitions. Is this a historical legacy? Something mandated by other elements of the FS pipeline? As a consequence of this behavior, if you have an oblique acquisition that was intentionally aligned to the actual anatomy of a given subject's brain (e.g., using AutoAlign to generate a AC-PC aligned acquisition), unless one manually alters the qform in the input NIFTI file to remove the "oblique" components of the xform, there will be an interpolation in the generation of the mri/orig.mgz, which brings with it blurring (i.e., the same sort of concerns that prompt one to use a single MPRAGE, rather than the average of two MPRAGEs) Just curious... thanks, -MH -- Michael Harms, Ph.D. Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave.Fax: 314-747-2182 St. Louis, MO 63110 Email: mha...@wustl.edu ___ 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] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences
Hello, When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects Directory, and then reran them using the FS5 recon-all stream. This updated their subject folders with the FS5 changes, but not in as many places as I would have thought. For example, on 6 test subjects, I created their FS5 folders from FS4 folders that I copied over and then ran the FS5 recon-all stream. I also created another copy of their FS5 folders from scratch. The average difference in their ICV values was -12,000 mm^3. Is it to be expected that FS5 reconstructions running on FS4 folders will not include all possible improvements? If I want to get an accurate an ICV measurement as possible, is it advisable to rerun all of my subjects in FS5, starting from scratch? As always, thank you for your valuable assistance! Jeff Sadino ___ 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.
Re: [Freesurfer] Overlay issues on freeview
Are you running the latest release version? Would it be possible to send us the surface file and the overlay file that crashes? Best, Ruopeng On 6/16/2011 3:34 PM, iac...@nmr.mgh.harvard.edu wrote: > Hi all, > I am trying to overlay a map on a specific subcortical structure (the > caudate). > > -I obtained the surface of the structure using the command: > > mri_tessellate structure.nii.gz 1 lh.structure.surf > > -then I projected my map on the surface using: > > mri_vol2surf --mov map.nii --regheader structure --hemi lh --surf > structure.surf --projdist 0 --fwhm 5 --out projected_map.mgz --interp > trilinear > > Everything seems to work properly. I am able to see the result using > tksurfer. > > However, when I try to overlay projected_map.mgz on lh.structure.surf > using freeview I experience a segmentation fault issue. > It seems that the software looks for the WM, the pial, the curv, etc > surfaces. > Obviously I don't have these information, since I am projecting the map > only on the caudate nucleus. > > Could you give me an advice about that? > > > Thanks > Maria > > > > > > ___ > 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 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] Overlay issues on freeview
Hi all, I am trying to overlay a map on a specific subcortical structure (the caudate). -I obtained the surface of the structure using the command: mri_tessellate structure.nii.gz 1 lh.structure.surf -then I projected my map on the surface using: mri_vol2surf --mov map.nii --regheader structure --hemi lh --surf structure.surf --projdist 0 --fwhm 5 --out projected_map.mgz --interp trilinear Everything seems to work properly. I am able to see the result using tksurfer. However, when I try to overlay projected_map.mgz on lh.structure.surf using freeview I experience a segmentation fault issue. It seems that the software looks for the WM, the pial, the curv, etc surfaces. Obviously I don't have these information, since I am projecting the map only on the caudate nucleus. Could you give me an advice about that? Thanks Maria ___ 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.
Re: [Freesurfer] Whole brain parcellation contd..
Thank you.
I just found this:
http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/
1) Is it better to extract the masks from the .mgz file (as explained on this
site) as opposed to converting the aparc+aseg-inhighres.mgz file to .nii.gz and
then extracting masks with FSL/AFNI?
2) Is there anyway to loop through all the labels instead of specifying by hand
in this command:
mri_label2vol –label ./lh.entorhinal.label –temp \
/Applications/freesurfer/subjects/${blindnum}/mri/rawavg.mgz –subject
${blindnum} –hemi lh –o \${blindnum}_lh_entorhinal.nii.gz –proj frac 0 1 .1
–fillthresh .3 –reg ../mri/register.dat
Thank you,
S
On 06/15/11, Douglas N Greve wrote:
>
>
> You are guaranteed not to have overlap regardless of what you do as
> there is only one label at each voxel. For Cortex, what you have is
> fine. For subcortical, you can use what is in
> $FREESURFER_HOME/ASegStatsLUT.txt. This has {Left,Right}-Cerebral-Cortex
> which can be ignored.
>
> doug
>
> Sudhin A. Shah wrote:
> > Hi,
> >
> > Is there anyway to know all the label #s that are in
> > aparc+aseg-inhighres.mgz.
> >
> > Thank you,
> >
> > S
> >
> > On 06/13/11, *"Sudhin A. Shah" * wrote:
> >> Hi Sorry for bothering you again, but I am not sure I understand.
> >>
> >> I was running whole brain correlation analysis (voxel by voxel). BUT
> >> for comparison purposes, I want to compute region by region
> >> correlation matrix.
> >> So, I want to divide up the brain into freesurfer parcellated regions
> >> - i.e. with no overlap, but with full coverage of whole brain.
> >>
> >> I have looked at FreeSurferColorLUT.txt and am confused because there
> >> are several sets and overlap (eg. 19 and 55 vs 2035..)
> >>
> >> If I use the following, can I ensure no overlap and full coverage?
> >> 1)Subcortical: 9-13, 16-19, 48-55, 58 - 59, 85,86
> >> 2)Cortex: 1002- 1034, 2002- 2034
> >>
> >> I am asking if there is an established list of whole brain
> >> parcellations before I rely on label names to choose the ROIS
> >>
> >> On 06/13/11, *Douglas N Greve * wrote:
> >>> Anything that is non-0 will cover the whole brain.
> >>> doug
> >>>
> >>> Sudhin A. Shah wrote:
> >>> > Hi, thank you. Is there a range in the labels that will ensure
> >>> that I am including the whole brain? I.e. I see labels for Cx, but
> >>> not subcortical..
> >>> > If I take labels 1001 to 2001 ( for eg ) will that cover whole brain?
> >>> >
> >>> > Thank you,
> >>> > S
> >>> >
> >>> >
> >>> >
> >>> > On Jun 13, 2011, at 10:59 AM, Douglas N Greve
> >>> wrote:
> >>> >
> >>> >
> >>> >> That is fine, or you can use mri_binarize with the --match
> >>> option. The numbers that correspond to each label can be found in
> >>> $FREESURFER_HOME/FreeSurferColorLUT.txt. You can also get at them
> >>> visual as I described in my previous email with tkmedit:
> >>> >>
> >>> >> tkmedit subject orig.mgz -aux aseg.mgz -aseg
> >>> >>
> >>> >> doug
> >>> >>
> >>> >>
> >>> >> Sudhin A. Shah wrote:
> >>> >>
> >>> >>> I mean that I am using FSL to create binary masks from
> >>> freesurfer parcellated regions. Unless there is a better way :)
> >>> >>>
> >>> >>> S
> >>> >>>
> >>> >>>
> >>> >>>
> >>> >>> On Jun 10, 2011, at 7:13 PM, Douglas N Greve
> >>> wrote:
> >>> >>>
> >>> >>>
> >>> >>>
> >>> What do you mean you are doing it with FEAT?
> >>>
> >>> Sudhin A. Shah wrote:
> >>>
> >>>
> >>> > Hello,
> >>> >
> >>> > I am a beginner so please bear with me. I want to obtain
> >>> binary masks for every region (Cortical + subcortical). I am using
> >>> FSL(feat) to do this BUT am not sure what the labels would be.
> >>> >
> >>> > I have looked at FreeSurferColorLUT.txt for
> >>> aparc+aseg-in-highres.mgz BUT do not know which labels to use to
> >>> avoid overlap and ensure full coverage.
> >>> >
> >>> > Thank you,
> >>> >
> >>> > S
> >>> >
> >>> >
> >>> >
> >>>
> >>> >
> >>> > ___
> >>> > Freesurfer mailing list
> >>> > Freesurfer@nmr.mgh.harvard.edu
> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> > (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
> >>> >
> >>> >
> >>> --
> >>> Douglas N. Greve, Ph.D.
> >>> MGH-NMR Center
> >>> gr...@nmr.mgh.harvard.edu
> >>> Phone Number: 617-724-2358 Fax: 617-726-7422
> >>>
> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>> (https://mail.nmr.mgh
Re: [Freesurfer] mri_annotation2labels
Hi Actually, its the opposite. I'm trying to get a volume from the label aka http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ On 06/16/11, Douglas N Greve wrote: > > If you're trying to create a label from a volume then use mri_cor2label. > doug > > Sudhin A. Shah wrote: > >Hi, > > > >I am trying to use this for the aparc+aseg-in-highres.mgz file instead of > >the default aparc > > > >mri_annotation2label --subject AY --hemi lh --outdir $fsfolder/AY/labels > >this works > > > >But how do I specify aparc+aseg-in-highres.mgz > > > >I tried --aparc+aseg-in-highres but it was not recognised.. > > > >Thank you, > >S > > > > > > > > > > > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >(https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer) > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > -- Sudhin A. Shah Postdoctoral Fellow Laboratory of Cognitive Neuromodulation Weill Cornell Medical College, NY,NY (212) 746-4514 ___ 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.
Re: [Freesurfer] mri_annotation2labels
If you're trying to create a label from a volume then use mri_cor2label. doug Sudhin A. Shah wrote: > Hi, > > I am trying to use this for the aparc+aseg-in-highres.mgz file instead > of the default aparc > > mri_annotation2label --subject AY --hemi lh --outdir > $fsfolder/AY/labels this works > > But how do I specify aparc+aseg-in-highres.mgz > > I tried --aparc+aseg-in-highres but it was not recognised.. > > Thank you, > S > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] pre-bedposted data in tracula
Hi Scott, You can do trac-all -prep first, to make sure you generate all the files needed for path reconstruction (including generating priors and masks from freesurfer recons), then move all your bedpostx files to the dmri.bedpostX as Anastasia mentioned and then do trac-all -path (for tract reconstruction). That should typically work. -Priti > Hi Scott - The bedpost outputs are expected to in a directory called > dmri.bedpostX under the subject's trac-all output directory. You can put > all your bedpost outputs there and proceed at your own risk! > > There's a description of other trac-all outputs from the steps before > bedpost here: > http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#OutputDirectoriesandFiles > > The bedpost step in trac-all would normally use eddy_corrected data and > and an anatomical brain mask from the FS recon, but otherwise there > shouldn't be other dependencies on previous steps. > > Hope this helps, > a.y > > On Wed, 15 Jun 2011, Scott Sorg wrote: > >> Hello, >> >> If I already ran bedpostx on my diffusion data, how can I skip this step >> in >> tracula and still get it to run smoothly. >> >> Thank you, >> >> Scott >> >> > ___ > 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 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.
Re: [Freesurfer] Custom color table overlay for ROI analysis
Hi Shashwath you can load a color table from the file menu in tksurfer. We almost never do this, so I'm not positive it works. The other thing you could do is read the annotation into matlab and change the color table that is stored in it, then write it back out. cheers Bruce On Thu, 16 Jun 2011, Shashwath Meda wrote: > Hi Alan - I dont see the instructions on how QDEC handles this? Could you > point me out to the wiki page that has this info. Again I dont want to draw > manual ROIs instead i want to assign my own value to the color tables > corresponding to the aparc labels in FS. > > On Wed, Jun 15, 2011 at 4:28 PM, Alan Francis wrote: > >> Hi Shashwath: >> >> The QDEC model in FS will allow you to do this. The website has all the >> details. >> >> best, >> >> Alan >> >> On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda >> wrote: >> >>> Hello Freesurfers - I just finished up with some group ROI analyses on >>> thickness and surface area measures derived from Freesurfer. Basically ran >>> the recon-all command, extracted individual ROI measures from the aparc and >>> aseg files and did my between-group analyses in SPSS. Now, i'd like to >>> display the significant ROIs on the brain with its corresponding p/F value. >>> What would be the easiest and most straightforward way to do this? >>> >>> >>> Thanks, >>> Shashwath >>> >>> >>> >>> ___ >>> 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
Re: [Freesurfer] Custom color table overlay for ROI analysis
Hi Alan - I dont see the instructions on how QDEC handles this? Could you point me out to the wiki page that has this info. Again I dont want to draw manual ROIs instead i want to assign my own value to the color tables corresponding to the aparc labels in FS. On Wed, Jun 15, 2011 at 4:28 PM, Alan Francis wrote: > Hi Shashwath: > > The QDEC model in FS will allow you to do this. The website has all the > details. > > best, > > Alan > > On Wed, Jun 15, 2011 at 5:02 PM, Shashwath Meda wrote: > >> Hello Freesurfers - I just finished up with some group ROI analyses on >> thickness and surface area measures derived from Freesurfer. Basically ran >> the recon-all command, extracted individual ROI measures from the aparc and >> aseg files and did my between-group analyses in SPSS. Now, i'd like to >> display the significant ROIs on the brain with its corresponding p/F value. >> What would be the easiest and most straightforward way to do this? >> >> >> Thanks, >> Shashwath >> >> >> >> ___ >> 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. >> >> > -- with regards, Shashwath Meda *** Imaging Genetics Analyst III 515-F Light Hall Vanderbilt University Medical Center Cell: (313) 505-6847 Off: (615) 875-3086 *** ___ 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.
Re: [Freesurfer] mri_cc error
Hi Vanessa, it looks like the error must have occurred earlier in the process as the input to mri_cc can't be read. Can you send the whole recon-all.log? cheers Bruce On Thu, 16 Jun 2011, Vanessa Lim wrote: > Hi, > > > > does anyone know what to do here please? I can see it in file manager. > > > > mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz CG > will read input aseg from aseg.auto_noCCseg.mgz > writing aseg with cc labels to aseg.auto.mgz > reading aseg from > /home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz > mghRead(/home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz, > -1): could not open file > mri_cc: could not read aseg volume from > /home/virtualuser/Desktop/freeSurfer/CG/CG/mri/aseg.auto_noCCseg.mgz > > also assuming I fix this error how do I resume from this point (or another > point) the rest of recon-all autorecon2? > > Thanks, > > Vanessa > ___ 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.
