[Freesurfer] Linear registration of subject meshes with FLIRT
In the FreeSurfer reliability paper, you recommend linearly registering the subject's meshes to each other and point to the Jenkinson paper. How actually is this done with FLIRT? Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mean FA values using wmparc
Once FA results are co-registered is there an easy way to use the wmparc.mgz to collect the mean FA values by region, or do we need to treat it like FMRI and make masks of each parcel and collect each mean separately? Dr Damian Jenkins Department of Clinical Neurology Oxford University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] design matrix : inter-run effetcs
Hi, Computing individual fMRI analysis (several runs) and looking at the design matrix (X.mat), I saw that only one regressor represents each condition. I was expecting that the number of regressors concerning a condition would be the number of runs (as SPM). There are "inter-run effect" regressors but is this better if I affect a different value for each of run and each condition (see examples below). Other question concerning design matrix : only 3 movement parameters included in the design matrix. Why 3 rather than the 6 computed during movement correction? Concerning inter-run effects and movement parameters, is there any advantage of reducing the number of regressors but having a less ideal model? 1 condition = 1regressor 0 = rest 1=conditionA 2=conditionB Pardagim files : RUN#1RUN#2RUN#3 000000 303030 606060 909090 120120120 151151151 181181181 211211211 241241241 271271271 300300300 330330330 360360360 390390390 422422422 452452452 482482482 512512512 542542542 570570570 1 condition = 1regressor / run 0=rest 1=conditionA run#1 2=conditionB run#1 3=conditionA run#2 4=conditionB run#2 5=conditionA run#3 6=conditionB run#3 Pardagim files : RUN#1RUN#2RUN#3 000000 303030 606060 909090 120120120 151153155 181183185 211213215 241243245 271273275 300300300 330330330 360360360 390390390 422424426 452454456 482484486 512514516 542544546 570570570 Frédéric ANDERSSON. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] can not see the pial surface using tksurfer
Hi, when I launched the command tksurfer to see the constructed pial surface, only a very small part of the surface can been seen in the window. I do not know how to fix the problem. Thanks! yczhang 2008-04-25 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] can not see the pial surface using tksurfer
If you have an Nvidia graphics card, you will need to update the driver. Try running nvidia-installer --update, as root (preferably have your sysadmin do this). Nick On Fri, 2008-04-25 at 21:25 +0800, yczhang wrote: > Hi, > when I launched the command tksurfer to see the constructed pial > surface, > only a very small part of the surface can been seen in the window. > I do not know how to fix the problem. > Thanks! > > > __ > yczhang > 2008-04-25 > ___ > 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
Re: [Freesurfer] VNC/GLX... what is really vncserver.glx
Another option to VNC is freenx. http://wiki.debian.org/freenx On Thu, 24 Apr 2008, Yaroslav Halchenko wrote: Thank you Tren, Actually Nick Schmansky at the time of original request pointed me out (I believe in an offlist conversation) to xf4vnc, I have built it then from CVS snapshot (there were/are no source tarballs), but it was segfaulting. Debian maintainer of VNC packages unfortunately isn't really eager to jump into burden of building yet another VNC package for Debian, so I just abandoned idea of using xf4vnc at that moment. May be now is a good timing to give it a shout again ;) On Thu, 24 Apr 2008, Tsung-Ren Huang wrote: Hi Yaroslav, You can comment out those lines regarding GLoverride. The real magic, as pointed out by Nick, is acutally the xf4vnc that can be downloaded from http://sourceforge.net/projects/xf4vnc . Tren d On Mon, 2007-01-15 at 23:27 -0500, Yaroslav Halchenko wrote: Thank you very much for providing the script. Now the question is what magic do you keep under /usr/lib64/GLoverride:/usr/lib/GLoverride because the rest of the script seems to be close to the standard vnc server script shipped originally (Debian maintainer introduced some changes as well but most only for parameter/configuration specifications). On Tue, 16 Jan 2007, Nick Schmansky wrote: Yaroslav, If you goto that RemoteAccess wiki page, and click on 'vncserver.glx', it will now allow you to download that script. You will have to modify it a bit: look for instances of /usr/pubsw/packages, which point to our installation of VNC. Nick -- --- Paul Rainesemail: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Unknown error
Okay, thanks for your help again Nick! Regarding the scan data: I am actually working with data collected by a previous member of our lab, and there were indeed some problems... (related to the SCIC algorithm on our GE scanner). So, our technician created a program to "uncorrect" the intensity scaling. The images he saved appear dark when we load them freesurfer, but we expected autorecon's intensity normalization would handle this. In fact, autorecon did successfully process 34 out of 35 scans. (the cortical surface appears quite decent for them, and the thickness values on our average subject appears to be within normal range...) I wonder if I should be concerned about our results due to this intensity issue... On Tue, Apr 22, 2008 at 2:42 PM, Nick Schmansky <[EMAIL PROTECTED]> wrote: > Jerry, > > At this point, I think Bruce will need to jump-in to answer (he is out- > of-town today). I think he will ask about your scan parameters, ie, how > is your scanner setup? It sounds as if something is not quite right in > the data coming-off the scanner. > > Nick > > > On Tue, 2008-04-22 at 14:26 -0400, Jerry Yeou-Wei Chen wrote: > > Thanks for the reply, Nick. I think you correctly identified the > > problem. > > nu.mgz is oriented correctly, but looks very dark... However, it looks > > decent if I adjust the brightness/contrast > > I have other scans that were processed without error, and the > > orig.mgz, and nu.mgz also appear quite dark (and the mri peaks are > > very low, too: 29, 46, 52, ...) Also, for those successfully > > processed, the brainmask.mgz looks decent as well. > > Perhaps this scan that exited with error was too dark to be corrected > > by the intensity normalization algorithm? > > > > - Jerry > > > > On Tue, Apr 22, 2008 at 1:22 PM, Nick Schmansky > > <[EMAIL PROTECTED]> wrote: > > Jerry, > > > > I'm not sure why it exited without giving a better message, > > but this is > > a clue why it exited: > > > > > > before smoothing, mri peak at 0 > > after smoothing, mri peak at 0, scaling input intensities by > > inf > > > > > > > > > > the mri peak is at zero, which is wrong (it should be around > > 116/117 or > > so). > > > > if you view nu.mgz (tkmedit -f nu.mgz), does it look ok? is > > it oriented > > correctly? > > > > Nick > > > > > > > > > > > > On Tue, 2008-04-22 at 12:28 -0400, Jerry Yeou-Wei Chen wrote: > > > Hello, > > > > > > I am having trouble deciphering why I got the error attached > > below. > > > Any suggestions would be greatly appreciated! > > > > > > Thanks, > > > - Jerry > > > > > > > > > > > > > > > Tue Apr 22 10:15:22 EDT 2008 > > > talairach_avi done > > > > > > cp transforms/talairach.auto.xfm transforms/talairach.xfm > > > > > > # > > > [EMAIL PROTECTED] Talairach Failure Detection Tue Apr 22 10:15:23 > > EDT 2008 > > > /scratch/freesurfer/subjects/17/s017/mri > > > > > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > > > > talairach_afd: Talairach Transform: transforms/talairach.xfm > > OK > > > (p=0.7072, pval=0.4932 >= threshold=0.0050) > > > > > > awk - > > > > > f /scratch/freesurfer/bin/extract_talairach_avi_QA.awk > /scratch/freesurfer/subjects/17/s017/mri/transforms/talairach_avi.log > > > > > > TalAviQA: 0.96840 > > > z-score: -2 > > > # > > > [EMAIL PROTECTED] Intensity Normalization Tue Apr 22 10:15:23 EDT > > 2008 > > > /scratch/freesurfer/subjects/17/s017/mri > > > > > > mri_normalize -g 1 nu.mgz T1.mgz > > > > > > using max gradient = 1.000 > > > reading from nu.mgz... > > > normalizing image... > > > talairach transform > > > 0.976 0.083 0.030 -136.866; > > > -0.072 1.053 0.164 -153.262; > > > -0.020 -0.109 1.085 -122.101; > > > 0.000 0.000 0.000 1.000; > > > INFO: Modifying talairach volume c_(r,a,s) based on > > average_305 > > > building Voronoi diagram... > > > performing soap bubble smoothing... > > > 3d normalization pass 1 of 2 > > > building Voronoi diagram... > > > performing soap bubble smoothing... > > > 3d normalization pass 2 of 2 > > > building Voronoi diagram... > > > performing soap bubble smoothing... > > > writing output to T1.mgz > > > 3D bias adjustment took 19 minutes and 44 seconds. > > > white matter peak found at 111 > > > gm peak at 88 (88), valley at 80 (80) > > > csf peak at 57, setting
[Freesurfer] total brain volume correction
Hello, I was curious if anyone had specific recommendations for correcting ROIs for total brain volume/ICV. From what I can tell, some groups correct each ROI by computing a ratio of ROI/total_brain_volume. Other groups, however, enter total brain volume as a covariate in their statistical models. Both methods seem reasonable, but it seems entering total brain size as a covariate may be more robust, controlling for potential interactions with other IVs (e.g. age, gender). Are there other strategies I am missing? Any advice is much appreciated! Thanks! -Ryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] lh.aparc.a2005s: S_subcentral_ant label
I have not looked at it before, but I do see that it exists on some of our subjects and not on others. Not sure why, except that it is a small structure that maybe gets crowded out. doug Juranek, Jenifer wrote: We recently started playing with the ?h.aparc.a2005s annotation files (fsv401). We noticed that in /freesurfer/subject/bert, the S_subcentral_ant label is not listed as a variable in the /stats/lh.aparc.a2005s output file. However, this variable name does *sometimes* appear in some of our study subjects. 1) Is this normal behavior? 2) Is it possible to add a FieldName index (analagous to the aseg.stats file) to facilitate detailed accountings of "empty" variables in the ?h.aparc.a2005s files? Many Thanks for any information you can provide, Jenifer ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] differences between last and new version of FS
Hi all, I'm trying the new version of FS for a study on multiple sclerosis that our group in Padova (Italy) is doing. When I give the command "mris_anatomical_stats -b -a aparc.annot etc..." to obtain the list of cortices, I obtain about 30 cortices, while in the last version of FS I could obtain about 80 cortices. So, can I obtain 80 cortices also with the new version of FS? How can I do it? Thanks Irene Mattisi Centre of Multiple Sclerosis, Hospital of Padova, Italy___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] differences between last and new version of FS
Irene, There are two parcellation schemes that freesurfer produces. The ? h.aparc.annot file contains 35 labels, while ?h.aparc.a2005.annot contains 78 labels. If you specify ... -a aparc.a2005s.annot in the mris_anantomical_stats command, you will get the 78 labels. The two schemes are described in the papers in the cortical parcellation section of the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/Articles ?h.aparc.annot - An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest ?h.aparc.a2005s.annot - Automatically Parcellating the Human Cerebral Cortex Nick On Fri, 2008-04-25 at 20:18 +0200, Irene Mattisi wrote: > Hi all, > I'm trying the new version of FS for a study on multiple sclerosis > that our group in Padova (Italy) is doing. > When I give the command "mris_anatomical_stats -b -a aparc.annot > etc..." to obtain the list of cortices, I obtain about 30 cortices, > while in the last version of FS I could obtain about 80 cortices. So, > can I obtain 80 cortices also with the new version of FS? How can I do > it? > Thanks > > Irene Mattisi > Centre of Multiple Sclerosis, Hospital of Padova, Italy > ___ > 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
[Freesurfer] Cannot execute any freesurfer GUI- Error of failed request:
FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-stable-pub-v4.0.3 Kernel info: Darwin 9.0.0 i386 ___ I recently updated to the newest release of freesurfer because for some reason I was unable to run qdec with 4.0.2. Though it appears that everything is setup exactly as it was before, I cannot execute any of the GUI (tkmedit, tksurfer, or qdec) I tried using the tutorial dataset to debug this. Below is an example command: tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Regardless of what I try to run, I get the following error: Couldn't create output file .xdebug_tkmeditX Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 17 Current serial number in output stream: 17 I already looked in the archives. I do have the most up to date version of X11. I am running this on my local machine, not via ssh, so this is not a display problem. All of my necessary variables are set (SUBJECTS_DIR, FREESURFER_HOME) and I have sourced $FREESURFER_HOME/ SetUpFreeSurfer.csh. Thnaks you in advance for your help. Jennifer Bramen -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cannot execute any freesurfer GUI- Error of failed request:
Jennifer, I think you have the PowerPC build, but your machine has an Intel processor. Try getting the one named: freesurfer-Darwin-leopard-i686-stable-pub-v4.0.3-full.dmg Although in principle (as stated by Apple) PowerPC code can be emulated on the Intel processor, in practice it looks like it doesnt work in all instances. Nick On Fri, 2008-04-25 at 14:05 -0700, Jennifer Bramen wrote: > FREESURFER_HOME: /Applications/freesurfer > > Build stamp: freesurfer-Darwin-leopard-stable-pub-v4.0.3 > > Kernel info: Darwin 9.0.0 i386 > ___ > > I recently updated to the newest release of freesurfer because for > some reason I was unable to run qdec with 4.0.2. Though it appears > that everything is setup exactly as it was before, I cannot execute > any of the GUI (tkmedit, tksurfer, or qdec) > > I tried using the tutorial dataset to debug this. Below is an example > command: > > > tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface > rh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > Regardless of what I try to run, I get the following error: > > > Couldn't create output file .xdebug_tkmeditX Error of failed request: > BadRequest (invalid request code or no such operation) > Major opcode of failed request: 128 (Apple-DRI) > Minor opcode of failed request: 1 () > Serial number of failed request: 17 > Current serial number in output stream: 17 > > > I already looked in the archives. I do have the most up to date > version of X11. I am running this on my local machine, not via ssh, so > this is not a display problem. All of my necessary variables are set > (SUBJECTS_DIR, FREESURFER_HOME) and I have sourced $FREESURFER_HOME/ > SetUpFreeSurfer.csh. > > Thnaks you in advance for your help. > > Jennifer Bramen > > -- > IMPORTANT WARNING: This email (and any attachments) is only intended for the > use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may subject > you to federal and state penalties. If you are not the intended recipient, > please immediately notify us by return email, and delete this message from > your computer. > -- > > ___ > 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
[Freesurfer] White Matter Regional Volumes
Hi Freesurfer Users, This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-?h- . Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats... If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link? Thank you Jennifer Bramen -- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
