Freesurfer

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30091 discussions

Fw: Making cuts using tksurfer
by Anupa AV 09 Apr '13

09 Apr '13

----- Forwarded Message ----- From: Anupa AV <av.anupa(a)yahoo.com> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Friday, April 5, 2013 11:24 AM Subject: Re: [Freesurfer] Fw: Making cuts using tksurfer Dear Sir, Kindly see the attachment. I tried to make it more clearer. Sorry for the previous incomplete attachment. Please give me some inputs to make coronal cut at y=26 (talairach coordinate). I'm also attaching a paper which I'm referring to. ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Anupa AV <av.anupa(a)yahoo.com> Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Thursday, April 4, 2013 5:40 PM Subject: Re: [Freesurfer] Fw: Making cuts using tksurfer Hi Anupa it's pretty hard to figure anything out from your images. What is wrong with using the cutting plane tool? You specify 3 points to define the plane, then a 4th to specify which side you want to keep cheers Bruce On Wed, 3 Apr 2013, Anupa AV wrote: > > ----- Forwarded Message ----- > From: Anupa AV <av.anupa(a)yahoo.com> > To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Sent: Wednesday, April 3, 2013 11:57 AM > Subject: Re: [Freesurfer] Making cuts using tksurfer > > Dear Sir, > > As you recommended, I have made a cut using plane option. Kindly see the > attachment. > My research interst is to make a coronal cut. > I've done it by merging the standard FreeSurfer parcellation labels of the > superior frontal gyrus, the rostral middle frontal gyrus and caudal > middle frontal gyrus (after loading DKatlas). > Then I cut the merged merged region using cut plane option. > Now I want to make a coronal cut at Talairach coordinate y=26(say), so as to > seperate dorsolateral prefrontal cortex from premotor cortex. > > > Can you please tell me how to make a coronal cut at y=26? > > Thanks in advance for your response. > > ____________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Anupa AV <av.anupa(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, April 1, 2013 6:15 PM > Subject: Re: [Freesurfer] MAking cuts using tksurfer > > you might try using a cutting plane instead of having to draw the entire > cut. > > cheers > Bruce > On Mon, 1 Apr 2013, Anupa AV wrote: > > > Dear All, > > > > How to explore the "cut" tools in freesurfer using tksurfer? > > I'd like to make a cut along the vertex on the cortical surface (say, > inflated) to divide medial and lateral components. > > How to do it after loading DKatlas labels and I want to cut along the > vertex to divde medial and lateral components.? > > > > Thanks in advance for your response. > > > > > > > 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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tksurfer partial overlays?
by raij＠nmr.mgh.harvard.edu 09 Apr '13

09 Apr '13

Hi, We need to display surface data (.w file). However, our algorithm failed to assign values for some vertices (and were therefore given the value of exactly zero), and to clearly differentiate those from vertices where we successfully computed values, we would like the vertices where we could not compute a value to be blank (=only the underlying anatomical surface shows). Normally I would just threshold the values to get rid of the "blank" vertices. However, we want to use tksurfer "offset 0.5" to shift the distribution such that all values smaller than 0.5 are shown as blue and all values larger than 0.5 in red/yellow. The offset also has the effect that the vertices where we were unable to compute a value will now have a value of exactly -0.5. Then, the question becomes how to make tksurfer paint only the vertices where we have a successfully computed value. After the shift, thresholding will no longer work because it only operates on values around zero. We have tried editing the .w file by both (i) removing the values from the vertices that we do not want painted, and (ii) removing the vertices (the entire line, vertex index plus value) from the file, but the tksurfer brain surface window still shows an overlay with a value of 0 in these vertices. Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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Tracula in freesurfer 5.2.0
by Gerit Pfuhl 09 Apr '13

09 Apr '13

Dear freesurfer experts, I was wondering whether we also need to upgrade the tutorial files when we upgraded from freesurer 5.1.0 to 5.2.0 and use Tracula I got as error that an ROI file of the Tutorial subject Diff001 does not exist. niiRead(): error opening file ../diffusion_tutorial/Diff001/ dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz ERROR: Could not read ./diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz everything before is fine and the path is sound Attached the logfile output (error message right at the end) Thanks for helping Gerit Pfuhl <http://team-arzgebirg.blogspot.com>

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GIFTI file
by Valtina Pouegue 09 Apr '13

09 Apr '13

Hi, I saw in the documentation that since the version 5.2.0 of Freesurferw ecan open and write .gii file. I have a surface in .gii and I would like open it on FS. The fact is that, I didn't find a way to do that in the documentation. Does anyone know a way? Thanks.

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Re: [Freesurfer] incomplete tracts
by Anastasia Yendiki 09 Apr '13

09 Apr '13

Are you running this on your own subject or the tutorial subject? Please include the freesurfer list on all emails with tracula questions. Thanks, a.y On Tue, 9 Apr 2013, Gerit Pfuhl wrote: > Dear Anastasia, > > I got some improvement by setting nctps to 7 (as I had done last week with version 5.1.0). > Now, we installed freesurfer 5.2.0 and I rerun one subject (changed drmirc file) > but I got the following message: > niiRead(): error opening file /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz > ERROR: Could not read /fastfs/igis/MRI_fs_rec_dti/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz > > diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz does not exist, so that must be a new data set.??? Though I saw that the > diffusion_tutorial page is from Sep 2012. > > Regards > Gerit > > > On 5 April 2013 18:23, Gerit Pfuhl <gerit.pfuhl(a)gmail.com> wrote: > Hi Anastasia, > > I will know more on monday, Then should also be able to upload files. > > Bests > Gerit > > > On 5 April 2013 17:37, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Gerit - If it's not an issue with the gradient table but instead a tractography initialization issue, I strongly recommend > running 5.2 with bbregister for the registration (which is the default in 5.2 anyway). > > You can also upload an example data set with issues (include: dmri, dmri.bedpostX, dlabel, dpath, scripts) here for me to take a > look: > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > Hope this helps, > a.y > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > Dear Anastasia, > > thanks for the help. There is also a line option in freeview. However we still have > brains with missing tracks, I rerun them with increasing the ncpts and registering to > bbr (since that is default in Tracula 5.2.). We are reasonable confident that our bvel > and bvac are correct, since we have roughly 20 cases out of 90 processed brains where > there are no missing tracts. Further sometimes only one tract is missing, sometimes it > is more severe. We could not find any correlation with recon-all problems or DTI raw > data issues (all but one were without moving artefacts). Since we are running bedpostx > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) might it be an issue > that is solved with installing the 5.2. version? Would that run in freesurfer 5.1.0? > I guess we need to change the dcmrirc files only a bit. > > Kind regards > Gerit Pfuhl > > > On 3 April 2013 16:59, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Benjamin - I'd look in a coronal view to see if the lines in the corpus > callosum follow the curvature of the corpus callosum, and in a sagittal > view to see if the lines in the cingulum follow the curvature of the > cingulum. Does this make sense? > > a.y > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > Dear Anastasia, > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our > gradient table is wrong but I am not really sure how to analyse > these informations. You wrote to Stefano the lines have to point in > the right direction and that the eigenvectors are not pointing along > his corpus callosum. Can you give me a more detailed description > what I have to do when I dislpay dtifit_V1 as lines, overlaid on > dtifit_FA. > > Thanks and kind regards > Benjamin > > _______________________________________________ > 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. > > > > > -- > http://gerit-orientation.blogspot.com > http://team-arzgebirg.blogspot.com > > > > > > -- > http://gerit-orientation.blogspot.com > http://team-arzgebirg.blogspot.com > > > > > -- > http://gerit-orientation.blogspot.com > http://team-arzgebirg.blogspot.com > >

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R: Re: incomplete tracts
by stdp82＠virgilio.it 09 Apr '13

09 Apr '13

Hi Anastasia, yes, I tried.I'm attacking the last configuration file that I used. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 9-apr-2013 1.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] incomplete tracts What registration methods are you using for the intra-subject and inter-subject registration? Have you tried the different options? On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-apr-2013 18.57 > A: <stdp82(a)virgilio.it> > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > What you say "again" you mean with 5.2? > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > yes, for some subject the low-b volume is in the end. > > Some subjects have again incomplete tracts. > > I'm attacking an example of configuration file that I'm using. > > I hope that you can check it please. > > > > Thanks, > > > > > > Stefano > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 5-apr-2013 18.45 > > A: <stdp82(a)virgilio.it> > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts > > > > > > Hi Stefano - In your case we determined that the ones that had the low-b > > volume in the end didn't run correctly, right? In that case, I didn't need > > to see anything, you were going to try running 5.2. > > > > a.y > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > Hi Anastasia, > > > could I send you the data of a subject that I don't run correctly? > > > > > > I still have some subjects with tracts incomplete and I do not know if > it depends > > from > > > my analysis or whether the images are not good. > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 5-apr-2013 17.37 > > > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > Hi Gerit - If it's not an issue with the gradient table but instead a > > > tractography initialization issue, I strongly recommend running 5.2 with > > > bbregister for the registration (which is the default in 5.2 anyway). > > > > > > You can also upload an example data set with issues (include: dmri, > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > > > > > Hope this helps, > > > a.y > > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > > > > > Dear Anastasia, > > > > > > > > thanks for the help. There is also a line option in freeview. However > we still > > have > > > > brains with missing tracks, I rerun them with increasing the ncpts and > registering > > > to > > > > bbr (since that is default in Tracula 5.2.). We are reasonable > confident that our > > > bvel > > > > and bvac are correct, since we have roughly 20 cases out of 90 > processed brains > > > where > > > > there are no missing tracts. Further sometimes only one tract is > missing, > > sometimes > > > it > > > > is more severe. We could not find any correlation with recon-all > problems or DTI > > raw > > > > data issues (all but one were without moving artefacts). Since we are > running > > > bedpostx > > > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) > might it be an > > > issue > > > > that is solved with installing the 5.2. version? Would that run in > freesurfer > > 5.1.0? > > > > I guess we need to change the dcmrirc files only a bit. > > > > > > > > Kind regards > > > > Gerit Pfuhl > > > > > > > > > > > > On 3 April 2013 16:59, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > Hi Benjamin - I'd look in a coronal view to see if the lines in > the corpus > > > > callosum follow the curvature of the corpus callosum, and in a > sagittal > > > > view to see if the lines in the cingulum follow the curvature of > the > > > > cingulum. Does this make sense? > > > > > > > > a.y > > > > > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > > > > > Dear Anastasia, > > > > > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because > our > > > > gradient table is wrong but I am not really sure how to analyse > > > > these informations. You wrote to Stefano the lines have to point > in > > > > the right direction and that the eigenvectors are not pointing > along > > > > his corpus callosum. Can you give me a more detailed description > > > > what I have to do when I dislpay dtifit_V1 as lines, overlaid on > > > > dtifit_FA. > > > > > > > > Thanks and kind regards > > > > Benjamin > > > > > > > > _______________________________________________ > > > > 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. > > > > > > > > > > > > > > > > > > > > -- > > > > http://gerit-orientation.blogspot.com > > > > http://team-arzgebirg.blogspot.com > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > >_______________________________________________ > 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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Re: [Freesurfer] Problem running Tracula longitudinal analysis
by Anastasia Yendiki 09 Apr '13

09 Apr '13

Hi Dylan - Can you send your trac-all.log file? (When the baselist is included in the dmrirc, otherwise you're just running the cross-sectional tractography.) Thanks, a.y On Mon, 8 Apr 2013, Dylan Nielson wrote: > I'm running CentOS 6.4. I don't know if it matters, but I tried running the > command from both bash and tcsh and they both give an error. Also, I did the > bedpost outside of freesurfer and then copied the outputs from that into the > freesurfer directories where they're supposed to go. The dcmric file will > run if I take out the baselist portion. > Any ideas you have would be great. > > Thanks, > > Dylan > > > On Mon, Apr 8, 2013 at 8:04 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Dylan - First of all kudos for being a brave early adopter :) > The only thing wrong with the dmrirc that I see is that there > can be only one bvecfile and bvalfile, not one per time point > (it's assumed that you used the same protocol for all time > points). > > That said, I don't think that's what's causing the error. What > operating system and version are you running this on? > > a.y > > On Sat, 6 Apr 2013, Dylan Nielson wrote: > > I am trying to run Tracula on a single subject with > two time points. I get the following Error > below. I suspect it is because I am not setting my > dmrirc file up correctly, but I cannot > figure out what the error is. I've copied my dmrirc > file below as well. > > Thanks, > > Dylan > > Command: > trac-all -prep -nocorr -nointra -c > dmrirc.long.RP0603 > > Error: > > trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd > ; > ERROR: flag ; unrecognized > -c > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd > ; trac-preproc -c > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local > -log > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log > -cmd > /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd > ; > > dmrirc.long > setenv SUBJECTS_DIR ~/fmri/RP0629_3T/freesurfer > set dtroot = ~/fmri/RP0629_3T/freesurfer > set subjlist = ( tp1002.long.002 \ > tp2002.long.002 ) > set baselist = ( 002 002 ) > set dcmroot = ~/fmri/RP0629_3T/freesurfer/ > set dcmlist = ( tp1002.long.002/dmri/dwi.nii.gz \ > tp2002.long.002/dmri/dwi.nii.gz ) > set bvecfile = ( tp1002.long.002/dmri/bvec \ > tp2002.long.002/dmri/bvec ) > set bvalfile = ( tp1002.long.002/dmri/bval \ > tp2002.long.002/dmri/bval ) > set dob0 = 0 > set doeddy = 0 > set thrbet = 0.5 > set doregflt = 0 > set doregbbr = 1 > set doregmni = 0 > set doregcvs = 1 > set cvstemp = cvs_avg35 > set cvstempdir = $FREESURFER_HOME/subjects > set usemaskanat = 1 > set pathlist = ( lh.cst_AS rh.cst_AS \ > lh.unc_AS \ > lh.ilf_AS \ > fmajor_PP fminor_PP \ > lh.atr_PP rh.atr_PP \ > lh.ccg_PP rh.ccg_PP \ > lh.cab_PP rh.cab_PP \ > lh.slfp_PP rh.slfp_PP \ > lh.slft_PP rh.slft_PP ) > set ncpts = (6 6 5 5 7 7 5 5 5 5 4 4 5 5 5 5) > set trainfile = > $FREESURFER_HOME/trctrain/trainlist.txt > set nstick = 2 > set nburnin = 200 > set nsample = 7500 > set nkeep = 5 > set reinit = 0 > > > > > 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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Rejoindre mon réseau sur LinkedIn
by Carl Anderson 09 Apr '13

09 Apr '13

LinkedIn ------------ Carl Anderson souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Carl Anderson http://www.linkedin.com/e/-qq80um-hfb2lg8j-68/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Carl Anderson http://www.linkedin.com/e/-qq80um-hfb2lg8j-68/rso/14130267/X9KR/name/664711… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hfb2lg8j-68/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Problem at tksurfer
by Roschinski, Benjamin 09 Apr '13

09 Apr '13

________________________________________ Von: Roschinski, Benjamin Gesendet: Donnerstag, 31. Januar 2013 13:37 An: freesurfer-owner(a)nmr.mgh.harvard.edu Betreff: Problem at tksurfer Dear Freesurfer users and experts, by doing the QC of our mri pictures, we found two unusual problems. The first problem is a strange appearance of insulas in many records of our patients by using recon checker as well as tksurfer. We would like to know, if this is a software problem or just a result of the young age(12-16) of our patients although we have a few older participants with the same problem. For a better understanding I have added a picture. Our second problem is a grey spot with "None" as description on the cuneus also in the parc pictures of recon checker and tksurfer. Do you have any ideas how to fix this problem? I have added a picture of this as well. I hope you can advise me how to fix these problems. Thanks and kind regards Benjamin

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Contrast file for cortical thickness 2 group 1 covariate analysis
by Alexandra Tanner 08 Apr '13

08 Apr '13

Dear Doug and Freesurfers, I'm running a group cortical thickness analysis covaried by age, and we're curious if there is a way to correlate thickness and age within groups and then look at whether or not there is a difference in the strength of the thickness/age relationship between groups. Originally the contrast file we used was the group-x-age.mtx (0 0 1 -1) looking at whether or not there was a difference between the group age slopes, but we then realized we're not interested in whether the slopes of the relationships are different, but rather if the strength of the cortical thickness/age relationship differs between groups. I ran mri_glmfit with an fsgd file that was set up as follows: GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables Age Input subject1 Group1 30 Input subject2 Group2 40 I've taken a look at the wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V) and can't seem to find a contrast file that does what we're looking for. Any advice on what sort of contrast file we should use, or whether we need to run a different analysis than glmfit, would be greatly appreciated! Thanks! Best, Alex

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