[Freesurfer] problem with labels
Dear Freesurfers, I have a problem with labels. I select a given Talairach coordinate that interests me, draw an approximately circular label around it in tksurfer, and save it. When I open that same label in tkmedit, the central Talairach coordinate is changed and the whole label is somewhat shifted. Am I missing something? Should I use mri_label2vol or some other command? Thanks very much in advance! Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23 ___ 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] problem with labels
Hi Irene, the label has to shift somewhat in tksurfer, since it will sample it onto the surface. Unless the entire label you drew was exactly on the surface boundary to begin with. cheers Bruce On Tue, 21 Dec 2010, Irene Altarelli wrote: > Dear Freesurfers, > > I have a problem with labels. I select a given Talairach coordinate that > interests me, draw an approximately circular label around it in > tksurfer, and save it. When I open that same label in tkmedit, the > central Talairach coordinate is changed and the whole label is somewhat > shifted. Am I missing something? Should I use mri_label2vol or some > other command? > > Thanks very much in advance! > Irene > > > ___ 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] {Spam?} Re: preproc-sess error
you can setenv FSLDIR /usr/pubsw/packages/fsl/3.3.7 then re-source the stable3 environment. doug jkus...@partners.org wrote: > Hi Doug, > > Thanks for your messages. We have to keep using stable3 for the rest of this > study. Does this mean we can just use a command to use the older version of > fsl to fix the ispl error? > > Thanks, > Jake > --Original Message-- > From: Douglas N Greve > To: swood...@nmr.mgh.harvard.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Cc: jkus...@partners.org > Subject: Re: [Freesurfer] preproc-sess error > Sent: Aug 2, 2010 1:54 PM > > If you're going to continue to use stable3 then you will need to have an > old version of FSL (the ip program is an FSL program from several > versions ago). Can you start using the new version of FSFAST? > > doug > > swood...@nmr.mgh.harvard.edu wrote: > >> Additional info: >> >> FREESURFER_HOME: /usr/local/freesurfer/stable3 >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-v3.0.5-20070714 >> >> RedHat release: CentOS release 5.5 (Final) >> >> Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 >> >> NMR Center info (/space/freesurfer exists): >> >> Does this give you the info you're looking for? >> >> Thanks, >> >> Sandra >> >> >> >> >> >> >>> which version are you using? >>> >>> swood...@nmr.mgh.harvard.edu wrote: >>> >>> Hello everyone, I keep encountering the same error when running some preprocessing steps (spatial smooting part). I run the command line: preproc-sess -s CD_DMRFASL_pat4 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 And I encounter this error: ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed Any help/advice would be much appreciated! Thanks, Sandra ___ 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 >>> >>> >>> >>> >>> >> >> > > -- 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.
[Freesurfer] help
Dear Colleague, Following is the error we get upon running the mri_annotation2label command r...@ubuntu:~# mri_annotation2label --subject one \ --h rh --labelbase ./label/aparc-rh ERROR: Option --h unknown r...@ubuntu:~# mri_annotation2label --subject one \ --hemi rh --labelbase ./label/aparc-rh ERROR: Option --hemi unknown Kindly address this error and give a reply as soon as possible Many thanks V.P.Subramanyam Rallabandi Senior R&D Engineer National Brain Research Centre, Manesar, Gurgaon, Haryana-122050, INDIA. ___ 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] help
that works for me: mri_annotation2label --subject bruce --hemi rh --labelbase . subject = bruce annotation = aparc hemi = rh labelbase = . surface = white Reading surface . . can you remove the \ in your command line? Bruce On Tue, 21 Dec 2010 subraman...@nbrc.ac.in wrote: > > Dear Colleague, > > > Following is the error we get upon running the mri_annotation2label command > > r...@ubuntu:~# mri_annotation2label --subject one \ --h rh --labelbase > ./label/aparc-rh > ERROR: Option --h unknown > r...@ubuntu:~# mri_annotation2label --subject one \ --hemi rh --labelbase > ./label/aparc-rh > ERROR: Option --hemi unknown > > Kindly address this error and give a reply as soon as possible > > Many thanks > > V.P.Subramanyam Rallabandi > Senior R&D Engineer > National Brain Research Centre, Manesar, > Gurgaon, Haryana-122050, INDIA. > > > ___ > 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] ICV differs systematically in repeated measurements
Hi Diederick, the ICV is computed from the linear talairach.xfm transform (including skull). There are all kinds of other talairach transforms produced by recon all, so make sure you are looking at the talairach.xfm (not ...lta or ..._with_skull.lta). You might want to read: http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV It is very likely that the clipping on your outlier image (missing cerebellum etc). produce an incorrect talairach.xfm and thus outlier ICV. Best, Martin On Tue, 2010-12-21 at 17:32 +0100, Diederick Stoffers wrote: > Hi Martin, > > > OK, I didn't expect different scanners/fieldstrengths to have that big > an effect on ICV. Given that there is a systematic bias, one would > expect a very high correlation between ICV at timepoint one and two. I > inspected a scatterplot and this was indeed the case, except for a > single outlier. The Tailairach registration looks fine for both > timepoints in this outlier. However, the scan at one timepoint was > badly planned, part of the cerebellum and brainstem are missing. Could > this explain the low ICV value in this subject? If not, what other > things should I check? > > > Cheers, > > > Diederick > > On 20 dec 2010, at 15:26, Martin Reuter wrote: > > > Hi Diederick, > > > > In a longitudinal study you need to ensure identical acquisition and > > processing, else you'll introduce a systematic bias. > > Some of my recent analyses indicate that even updating the software > > on the scanner can bias your results. Hardware changes are worse. > > > > Best Martin > > > > On Dec 20, 2010, at 6:48 AM, Diederick Stoffers > > wrote: > > > > > Hi all, > > > > > > I have a dataset with AD patients that were scanned twice, once at > > > 1.5T and once at 3T at an interval of a few years. The ICV values > > > are lower for almost all subjects at timepoint two (FS 5.0). Isn't > > > ICV in the later FS versions supposed to be independent of brain > > > volume as it is based on a scaling factor derived from the > > > Tailairach transform of the skull? Many thanks! > > > > > > Cheers, > > > > > > Diederick > > > ___ > > > 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] ICV differs systematically in repeated measurements
As I said, there are several talairach transforms. You need to look at the talairach.xfm. The wiki says: To check the quality of the registration file talairach.xfm file: cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk Martin On Tue, 2010-12-21 at 20:12 +0100, Diederick Stoffers wrote: > Hi Martin, > > > I read the wiki on eTIV after finding this outlier. I used > > > tkregister2 --mgz --s subject --fstal --surf orig > > > to check the registration, that looked pretty decent. Any other > pointers? > > > Thanks! > > > Diederick > > > > On 21 dec 2010, at 17:40, Martin Reuter wrote: > > > Hi Diederick, > > > > the ICV is computed from the linear talairach.xfm transform > > (including > > skull). There are all kinds of other talairach transforms produced > > by > > recon all, so make sure you are looking at the talairach.xfm > > (not ...lta > > or ..._with_skull.lta). > > > > You might want to read: > > http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV > > > > It is very likely that the clipping on your outlier image (missing > > cerebellum etc). produce an incorrect talairach.xfm and thus outlier > > ICV. > > > > Best, Martin > > > > On Tue, 2010-12-21 at 17:32 +0100, Diederick Stoffers wrote: > > > Hi Martin, > > > > > > > > > OK, I didn't expect different scanners/fieldstrengths to have that > > > big > > > an effect on ICV. Given that there is a systematic bias, one would > > > expect a very high correlation between ICV at timepoint one and > > > two. I > > > inspected a scatterplot and this was indeed the case, except for a > > > single outlier. The Tailairach registration looks fine for both > > > timepoints in this outlier. However, the scan at one timepoint > > > was > > > badly planned, part of the cerebellum and brainstem are missing. > > > Could > > > this explain the low ICV value in this subject? If not, what other > > > things should I check? > > > > > > > > > Cheers, > > > > > > > > > Diederick > > > > > > On 20 dec 2010, at 15:26, Martin Reuter wrote: > > > > > > > Hi Diederick, > > > > > > > > In a longitudinal study you need to ensure identical acquisition > > > > and > > > > processing, else you'll introduce a systematic bias. > > > > Some of my recent analyses indicate that even updating the > > > > software > > > > on the scanner can bias your results. Hardware changes are > > > > worse. > > > > > > > > Best Martin > > > > > > > > On Dec 20, 2010, at 6:48 AM, Diederick Stoffers > > > > wrote: > > > > > > > > > Hi all, > > > > > > > > > > I have a dataset with AD patients that were scanned twice, > > > > > once at > > > > > 1.5T and once at 3T at an interval of a few years. The ICV > > > > > values > > > > > are lower for almost all subjects at timepoint two (FS 5.0). > > > > > Isn't > > > > > ICV in the later FS versions supposed to be independent of > > > > > brain > > > > > volume as it is based on a scaling factor derived from the > > > > > Tailairach transform of the skull? Many thanks! > > > > > > > > > > Cheers, > > > > > > > > > > Diederick > > > > > ___ > > > > > 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] Freesurfer longitudinal analysis
Hi, I want to use FreeSurfer to analyze a longitudinal study. For each subject in my study, I already used FreeSurfer 4.2 to perform the cross-sectional analysis. However, FreeSurfer 4.2 did not have a longitudinal pipeline. Therefore, I want to use FreeSurfer 4.5 for this purpose (in the FreeSurfer wiki, it said the longitudinal pipeline in 5.0 is broken). My question is: A) Should I redo the cross-sectional analysis using FreeSurfer 4.5 OR B) I just run 'recon-all -base' and 'recon-all -long' using FreeSurfer 4.5, based on the cross-sectional results from version 4.2. Thanks, Rong ___ 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] orig/conform
Is there a quick way to transform the orig.mgz data back to the 'original" orientation of the orig/001.mgz data set? i.e., undo the conform? Greg ___ 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] orig/conform
That's what the rawavg.mgz is. You can use mri_convert with -rl rawavg.mgz to realize other conformed volumes back to that space On Dec 21, 2010, at 5:50 PM, "Harrington, Gregory S." wrote: > Is there a quick way to transform the orig.mgz data back to the > 'original" orientation of the orig/001.mgz data set? i.e., undo the > conform? > > Greg > > > ___ > 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] volume - surface shift in tkmedit
Dear all I would like to write an MRI anatomical volume and a surface in freesurfer format. The surface is correspondent to the white matter tessellation, while the volume represents T1 anatomical slices, both obtained from softwares external to FreeSurfer. Using the two functions save_mgh.m and write_surf.m from the freesurfer matlab interface files I am able to write the variables in the proper freesurfer folders. In the original nifti format volume and surface match both in voxel space and in millimiters space, but as soon as i visualize them in tkmedit the surface is shifted. Any clue why this happens? Is there any matrix that automatically translates the surface coordinates when it is read in tkmedit? I hope to get your feedback soon Best regards Cristiano ___ 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.
