Hi Melonee, Please record my off Campus work hrs this morning at OU. IN 9:30 AM and out 1:10 PM. I have logged into LIBR when I entered so that should be in records. Let me know if you may have any question. Thanks, Rashmi
On 2/11/13 8:39 AM, "[email protected]" <[email protected]> wrote: >Send Freesurfer mailing list submissions to > [email protected] > >To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >or, via email, send a message with subject or body 'help' to > [email protected] > >You can reach the person managing the list at > [email protected] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. A question regarding a "nii-read" error I get when running a > script for FA values output (Rotem Saar) > 2. re conversion (Linn Mittlestein) > 3. LME matlab toolbox - smooth error (Yolanda Vives) > 4. thickness and area in aparc.stats and mri_glmfit (Wolff Schlotz) > 5. trac-all -path error ([email protected]) > 6. R: trac-all -path error ([email protected]) > 7. Re: re conversion (Bruce Fischl) > 8. Antw: Re: thickness and area in aparc.stats and mri_glmfit > (Wolff Schlotz) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 11 Feb 2013 11:50:15 +0200 >From: Rotem Saar <[email protected]> >Subject: [Freesurfer] A question regarding a "nii-read" error I get > when running a script for FA values output >To: [email protected] >Message-ID: > <CAMjFEmY3_B2G7VVqeGTcptYmS4cdAAdgbka6UTR=-1W_p=g...@mail.gmail.com> >Content-Type: text/plain; charset="iso-8859-1" > >Hi, > >My name is Rotem, I'm a PhD. student and recently started to work with >freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION >For several weeks, I have been trying to operate a script for FA values, >with no success, and would really appreciate your help with shading some >light regarding the problem and it's solution. >I have a data set, after an anatomical segmentation (file is attached, >named "Anatomical segmentation for fs", this is the script I'm using for >brain anatomical segmentation). What I'm trying to run now is the DTI >script, in which I run commands that at least for my understanding spouse >to give me at the end a table with all the FA values for each brain region >(ROI). The script I'm using to do this is attached and called >"DTI_RUN_NEW_FOR_FS". >*After running phase 5*, in which a mask file should be created (indeed I >have checked and the file is created in the same folder it should be): > >fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_mask >/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii >/usr/local/freesurfer/subjects/FOLDER_NAME/mri/brainmask.mgz >/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii >DoAbs = 0 >Found 16777216 voxels in mask >Writing masked volume to >/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii...d >one. > >*I run phase 6, and then get the following error message:* > >fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_segstats --seg >/usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab >$FREESURFER_HOME/FreeSurferColorLUT.txt --i >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii >--sum >/usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME > >$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ >cwd >cmdline mri_segstats --seg >/usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab >/usr/local/freesurfer/FreeSurferColorLUT.txt --i >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii --sum >/usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME >sysname Linux >hostname fmri4-P67A-D3-B3 >machine i686 >user fmri4 >Loading /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz >Loading >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii >niiRead(): error opening file >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii >ERROR: loading >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii > >I think the problem is between phase 5 and 6, and is related to file >format >(.nii) but don't have a hint regarding what can I do to solve this:( Can >someone please write me the correct code line ? > >I would really appreciate your kind help since I run out of ideas for >solutions. > >Thanks in advance, > >Rotem >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >5d2265f9/attachment-0001.html >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: Anatomical segmentation for fs >Type: application/octet-stream >Size: 1494 bytes >Desc: not available >Url : >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >5d2265f9/attachment-0002.obj >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: DTI_RUN_NEW_FOR_FS >Type: application/octet-stream >Size: 1738 bytes >Desc: not available >Url : >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >5d2265f9/attachment-0003.obj > >------------------------------ > >Message: 2 >Date: Mon, 11 Feb 2013 10:55:45 +0000 >From: Linn Mittlestein <[email protected]> >Subject: [Freesurfer] re conversion >To: [email protected] >Message-ID: > <CAPxBFywUrOAyRJ3_r87pGsYswnvwntv7BL7MKi+AYArGuCqX=q...@mail.gmail.com> >Content-Type: text/plain; charset="iso-8859-1" > >Dear freesurfer experts, > >I have a question. I am trying to complete the longitudinal tutorial, and >in freeview tutorial it states: > > "In order to analyze your longitudinal data, you have different options. >You could, e.g., open the stats text files in each >tpN.long.templateID/stats/ dir, containing statistics such as volume of >subcortical structures or thickness averages for cortical regions. These >statistics can be fed (after conversion) into statistical packages to run >whatever analysis you are interested in" > >I am wondering what exactly "after conversion" refers to ( I encountered >the same phase in the other recon option (ie cross-sectional). I was under >the impression that the values from the stats files are the ones to use; >thus what does after conversion refer too? > >Kind Regards, Linn >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >45094eff/attachment-0001.html > >------------------------------ > >Message: 3 >Date: Mon, 11 Feb 2013 12:14:58 +0100 >From: Yolanda Vives <[email protected]> >Subject: [Freesurfer] LME matlab toolbox - smooth error >To: [email protected] >Message-ID: > <cakrnvdsvsjfgxmppwe8ccpee0o-8vuwcwcv+85nc7cvkfp+...@mail.gmail.com> >Content-Type: text/plain; charset=ISO-8859-1 > >Dear all > >I am a new user of the LME matlab toolbox and I have an error when >running lme_lowessPlot due to the smooth function. Do I need a >particular matlab toolbox to run this function? I have not seen any >smooth function in the LME toolbox. > >Error in ==> lme_lowessPlot at 49 > ybw = smooth(st,dat(ix),bw,'rlowess'); > >Error in ==> LME at 14 >lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2)); > >Thank you in advance, >Yolanda > > >------------------------------ > >Message: 4 >Date: Mon, 11 Feb 2013 13:37:29 +0100 >From: "Wolff Schlotz" <[email protected]> >Subject: [Freesurfer] thickness and area in aparc.stats and mri_glmfit >To: <[email protected]> >Message-ID: <[email protected]> >Content-Type: text/plain; charset="us-ascii" > >Dear Freesurfer experts, > >I tested associations between a continuous predictor and thickness and >area in qdec (and command line mri_glmfit, which gives the same results) >and found a cluster being negatively associated with thickness >orbitofrontal, but nothing for area orbitofrontal. After exporting mean >thickness and area values from aparc.stats into Stata, consistent with my >expectation I found a significant negative correlation with my predictor >for thickness. However, I also found a significant positive association >between birth weight and area. > >To check what might be wrong I tested correlations between mean >medialorbitofrontal thickness from rh.aparc.thickness and thickness in >qdec and did the same for area. As expected, large average thickness >values were positively associated with thickness in medialoribotfrontal >and adjacent areas (see attached qdec screenshot thickness.png), but >there were no associations using area (see attached qdec screenshot >area.png). My expectatioin was that there should be positive area >associations similar to those for thickness. > >Hence my question: Is this expectation correct? If yes, why this >discrepancy between thickness and area? > >Thank you. > >Wolff >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >16f2d402/attachment-0001.html >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: area.png >Type: image/png >Size: 101712 bytes >Desc: not available >Url : >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >16f2d402/attachment-0002.png >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: thickness.png >Type: image/png >Size: 115984 bytes >Desc: not available >Url : >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >16f2d402/attachment-0003.png > >------------------------------ > >Message: 5 >Date: Mon, 11 Feb 2013 14:42:11 +0100 (CET) >From: <[email protected]> >Subject: [Freesurfer] trac-all -path error >To: [email protected] >Cc: [email protected] >Message-ID: <[email protected]> >Content-Type: text/plain; charset="utf-8" > >Hi list, >I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I >have this error: >Loading mask from >/Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+as >eg_mask.bbr.nii.gzLoading BEDPOST parameter samples from >/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostXniiRead >(): error opening file >/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged >_ph1samples.nii.gzERROR: Could not read >/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged >_ph1samples.nii.gz >>From >>http://www.mail-archive.com/[email protected]/msg22066.html >>I'm deducing that the error may be related trace-all upload. >I have doing this upload but I visualize always the same error. >I attached tract-all uploades file that live in >/Applications/freesurfer/bin. >Please, could you check it? >I have also other question. May I run the second step of trac-all >(bedpostx) using FSL on other pc? In this way, could I directly run in >FSL dmri folder? Do you think that I should rename some files? >Thanks, > >Stefano >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >a9caf345/attachment-0001.html > >------------------------------ > >Message: 6 >Date: Mon, 11 Feb 2013 14:59:11 +0100 (CET) >From: <[email protected]> >Subject: [Freesurfer] R: trac-all -path error >To: <[email protected]> >Cc: [email protected] >Message-ID: <[email protected]> >Content-Type: text/plain; charset="utf-8" > >I'm attaching my trac-all file for check.Thanks, >Stefano > > > >----Messaggio originale---- > >Da: [email protected] > >Data: 11-feb-2013 14.42 > >A: <[email protected]> > >Cc: <[email protected]> > >Ogg: [Freesurfer] trac-all -path error > > > >Hi list, >I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I >have this error: >Loading mask from >/Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+as >eg_mask.bbr.nii.gzLoading BEDPOST parameter samples from >/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostXniiRead >(): error opening file >/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged >_ph1samples.nii.gzERROR: Could not read >/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged >_ph1samples.nii.gz >>From >>http://www.mail-archive.com/[email protected]/msg22066.html >>I'm deducing that the error may be related trace-all upload. >I have doing this upload but I visualize always the same error. >I attached tract-all uploades file that live in >/Applications/freesurfer/bin. >Please, could you check it? >I have also other question. May I run the second step of trac-all >(bedpostx) using FSL on other pc? In this way, could I directly run in >FSL dmri folder? Do you think that I should rename some files? >Thanks, > >Stefano > > > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >dc3976ba/attachment-0001.html >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: trac-all >Type: application/octet-stream >Size: 60757 bytes >Desc: not available >Url : >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >dc3976ba/attachment-0001.obj > >------------------------------ > >Message: 7 >Date: Mon, 11 Feb 2013 09:20:58 -0500 (EST) >From: Bruce Fischl <[email protected]> >Subject: Re: [Freesurfer] re conversion >To: Linn Mittlestein <[email protected]> >Cc: [email protected] >Message-ID: > <[email protected]> >Content-Type: text/plain; charset="iso-8859-1" > >Hi Linn > >I think it means after you convert the stats file into a format that >whatever stats package you are going to use can read. > >cheers >Bruce >On Mon, 11 Feb 2013, >Linn Mittlestein wrote: > >> Dear freesurfer experts, >> >> I have a question. I am trying to complete the longitudinal tutorial, >>and in >> freeview tutorial it states: >> >> ?"In order to analyze your longitudinal data, you have different >>options. >> You could, e.g., open the stats text files in each >> tpN.long.templateID/stats/ dir, containing statistics such as volume of >> subcortical structures or thickness averages for cortical regions. These >> statistics can be fed (after conversion) into statistical packages to >>run >> whatever analysis you are interested in" >> >> I am wondering what exactly "after conversion" refers to ( I >>encountered the >> same phase in the other recon option (ie cross-sectional). I was under >>the >> impression that the values from the stats files are the ones to use; >>thus >> what does after conversion refer too? >> >> Kind Regards, Linn >> >> > >------------------------------ > >Message: 8 >Date: Mon, 11 Feb 2013 15:39:15 +0100 >From: "Wolff Schlotz" <[email protected]> >Subject: [Freesurfer] Antw: Re: thickness and area in aparc.stats and > mri_glmfit >To: <[email protected]> >Message-ID: <[email protected]> >Content-Type: text/plain; charset="us-ascii" > >Dear Anderson (and all), > >Many thanks for your reassuring response, but I am still puzzled about >the lack of association between mean area (rh_medialorbitofrontal_area) >and area in qdec (see area.png). I thought that technically there must be >larger areas for vertices within medialorbitofrontal? > >Best wishes, >Wolff > >>>> "Anderson M. Winkler" <[email protected]> 11.02.2013 14:22 >>> >Dear Wolff, > >There is nothing wrong with your results. Your finding is one more >confirmation that thickness and area are indeed different traits, which >are influenced differently by different genetic and/or environmental >factors, and should not be confused one with another. They represent >different aspects of brain morphology and its development, and can (and >should) be analyzed and interpreted each on its own right. > >It is also evidence that more power can be gained by using these two >measurements separately, rather than mixed up as in methods that only >measure gray matter volume. > >Assuming you did everything else correctly, your results look perfectly >fine to me. > >All the best! > >Anderson > > > >2013/2/11 Wolff Schlotz <[email protected]> > > >Dear Freesurfer experts, >I tested associations between a continuous predictor and thickness and >area in qdec (and command line mri_glmfit, which gives the same results) >and found a cluster being negatively associated with thickness >orbitofrontal, but nothing for area orbitofrontal. After exporting mean >thickness and area values from aparc.stats into Stata, consistent with my >expectation I found a significant negative correlation with my predictor >for thickness. However, I also found a significant positive association >between birth weight and area. >To check what might be wrong I tested correlations between mean >medialorbitofrontal thickness from rh.aparc.thickness and thickness in >qdec and did the same for area. As expected, large average thickness >values were positively associated with thickness in medialoribotfrontal >and adjacent areas (see attached qdec screenshot thickness.png), but >there were no associations using area (see attached qdec screenshot >area.png). My expectatioin was that there should be positive area >associations similar to those for thickness. >Hence my question: Is this expectation correct? If yes, why this >discrepancy between thickness and area? >Thank you. > > >Wolff > >_______________________________________________ >Freesurfer mailing list >[email protected] >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. > > > >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >e839c8d4/attachment.html >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: area.png >Type: image/png >Size: 101712 bytes >Desc: not available >Url : >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >e839c8d4/attachment.png >-------------- next part -------------- >A non-text attachment was scrubbed... >Name: thickness.png >Type: image/png >Size: 115984 bytes >Desc: not available >Url : >http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130211/ >e839c8d4/attachment-0001.png > >------------------------------ > >_______________________________________________ >Freesurfer mailing list >[email protected] >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >End of Freesurfer Digest, Vol 108, Issue 12 >******************************************* _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
