Re: [Freesurfer] Error upon trying to load NIFTI image in freeview
Thanks for your reply Yaniv! That is how I initially tried loading the NIFTI volumes (via the GUI, File|Load), but in the meantime I discovered what the problem was: there were spaces in the name of the folder containing the image, and apparently non-Windows OSs such as Xubuntu don't deal well with that! For future reference, as soon as you eliminate spaces - as well as possibly other'forbidden' characters from the file/folder name, FreeView will load the image with no problems. Tudor On 6 December 2012 00:44, Yaniv Kaufman kaaniv.kaauf...@gmail.com wrote: Hi Tudor, I am not very experienced with Freeview, but did you try typing freeview in the command line and using the File-Load Volume… from the GUI? If that doesn't work maybe you can give me the exact command you used. Hope I could help. Regards, Yaniv On 06/12/2012, at 1:47 AM, Tudor Popescu tud...@gmail.com wrote: Hi everyone, I tried opening a NIFTI (.nii.gz) image in freeview, but it gives me repeated Failed to load image name errors. That same image loads fine in FSLview, but even when trying with other NIFTI images, I get the same error. The default image (/home/virtualuser/freesurfer/subjects/bert/mri/brainmask.mgz) opens fine in freeview. I use FreeSurfer v5.1.0 on Xubuntu 9.10, running through VirtualBox on WinXP. Many thanks for any help! Tudor ___ 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 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] Missing Insula and mri_label2vol
Thanks Doug, now it works!! for mac use ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.mac ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux32 doug On 12/05/2012 05:11 AM, Jos? ?ngel Pineda wrote: Hi again, Sure I did set the permissions for execution, and also for this new one I am still having the same error. /Exec format error. Binary file not executable/. I tried this on two macs (OSX Snow Leopard). I am still thinking that this is a compilation issue of the script, that is just compiled for linux. Thanks for your help Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux32 On 12/04/2012 12:13 PM, Sarosh, Cyrus wrote: Doug, I am unsure if Jose did this in his attempts to get it to work, but I ran this command after downloading and receiving this error initially and even after running this command I still receive the same error in the Windows virtual machine version of FreeSurfer. Any other ideas? Thanks, Cyrus -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, December 04, 2012 11:58 AM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) Hi Jose, did you set the permissions to be executable? chmod a+x mri_label2vol doug On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote: Doug, I am also curious about this mri_label2vol upgrade. Will this work on the Windows virtual machine version of FreeSurfer? I downloaded and placed it in the FREESURFER/bin directory, but when trying to run it I receive an error that states: Exec format error. Binary file not executable. Thanks for your help. Cyrus *From:*freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Jos? ?ngel Pineda *Sent:* Tuesday, December 04, 2012 9:07 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] (no subject) Thanks Doug, I already downloaded the new script for mri_label2vol, but it seems it is just compiled for linux, as I cannot execute it in my Mac. If it is so, could you please upload another compiled for mac, or source. Thanks Jose For the missing insula problem, try using a newer version of mri_label2vol ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_labe l2vol The 2nd problem is not so easy to fix. You might be better off using aparc+aseg.mgz as input to mri_label2vol instead of the surface annotation. doug On 12/3/12 10:35 AM, Jos? ?ngel Pineda wrote: Dear experts, I am registering cortical labels from Talairach coordinates to my native T1. For doing this, I have run the next script lines: tkregister --targ brainmask.mgz --mov highres_brain.nii.gz --reg T1FS2Highres.dat --regheader --noedit mri_label2vol --annot rh.aparc.annot --temp highres_brain.nii.gz --reg T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject FS --proj frac 0 1 .1 --fillthresh .3 and the same for the left hemi. However I am finding two problems at the result. First Insula is missing for both hemispheres, and second the cortical ROIs have the shape of the figure attached, e.g. there are many voxels empty Im?genes integradas 1 I found in previous topics, that the mri_label2vol, was updated as it left last volume from the list out of the conversion. I tried to download it, but it is just compiled for linux, and since Im working with mac I am not able to run it. Could you please give me any comments to solve the problem with the missing voxels. About the problem with the insula, the other option is to just extract it with mri_annotation2label, but
[Freesurfer] Hippocampus volume
Dear FS team, After I ran the recon-all to get the total cortical thickness, the volume of the left hypocampus ( = the number of voxels) equals to 2166 which I thought should be the total hippocampal volume. But if we add all the voxel numbers from the hippocampal subfield I will get a much larger number so I wonder which one represents the true total volume in terms of number of voxels. Can you also please advise how can I get differentiated hipocampus segmentation in form of head and body. Thank you. Antonella___ 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] Running recon-all on a series of scans
Hi, Is it possible to run recon-all on a series of scans? I have multiple scans that I want to process longitudinally. The .nii files have all been converted to .mgz files and labelled sequentially (i.e., 001.mgz, 002.mgz, etc.) in /Applications/freesurfer/subjects/subjid/mri. I've tried running recon-all on this whole folder with the command line: recon-all -subjid subjid -all, but it does not execute properly. Do I have to run each of these scans separately using recon-all (i.e., do I need to use a separate terminal for each scan)? Thank you in advance for your time and help. ___ 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] Longitudinal analysis - contrast
Yes,
in 5.2 there should be the two new options --qdec and --qdec-long
to allow passing qdec tables both in the regular cross sectional and in
the longitudinal format in addition to the existing other ways of
passing subjects lists (--s or --fsgd or --f ).
Now care needs to be taken in the longitudinal setting. What you want is
to get the files (e.g. thickness) from the *.long.base directories
into the target (e.g fsaverage space). Not from the cross sectional
directories!
For this you will be able to use the longitudinal qdec file (with a
column of 'fsid' and 'fsid-base' to group time points into subjects, see
wiki).
In 5.1 you should do the following:
create a text file with each longitudinal id (containing
the .long.base ) per line and pass it using the --f flag.
So in the example below you'd write:
002.long.002_base
003.long.003_base
003_m6.long.003_base
You can use a simple shell command to get such a list from a
longitudinal qdec file:
cat long.qdec.table.txt | awk '{if ($1 != fsid substr($1,0,1) !=
#) printf(%s.long.%s\n, $1, $2)}' outsubjectsfile.txt
Then preproc will do its job. The order of subjects needs to be
identical to the qdec file that you use to run the LME matlab tools to
ensure thickenss maps are stacked in the same order as you pass the
covariates.
Best, Martin
On Thu, 2012-12-06 at 04:27 +, jorge luis wrote:
Hi Alex
I think that Martin added the flag --qdec to mris_preproc for version
5.2. Martin, could you confirm this please?
The code for building the study design matrix X that is in the wiki is
just an example of how lme tools can be used for that purpose but the
actual instance of your code will depend on your particular Qdec
table. For instance, usually, Freesurfer's longitudinal Qdec tables
are of the form:
fsidfsid-base sIDtime group...
002002_base 0020 0
003003_base0030 1
003_m6003_base0030.56 1
003_m12 003_base0031.121
003_m24 003_base0032.2 1
005005_base00500
005_m6005_base0050.45 0
005_m12 005_base 0051.2 0
were “fsid” is the Freesurfer's ID, “fsid-base” is the name of the
subject's specific template, sID is the subject-specific ID uniquely
identifying each subject, “time” is the time covariate and group is
the group membership covariate (there can be more covariates of
course). I suppose that you processed your longitudinal MRI scans
using a Qdec table similar to that.
You can read that Qdec table into Matlab:
Qdec = fReadQdec('qdec.table.dat');
Now you need to build your numeric design matrix X from the cell
string array Qdec to represent a specific longitudinal design. Here
you don't need the columns fsid and fsid-base in Qdec so you simply
remove them:
Qdec = rmQdecCol(Qdec,1);
Qdec = rmQdecCol(Qdec,1);
The you can grab the subject-specific ID:
sID = Qdec(:,1);
and then remove that column:
Qdec = rmQdecCol(Qdec,1);
You can now convert your cell string array Qdec to a numeric matrix:
M = Qdec2num(Qdec);
Here, the data in M is already ordered according to time for each
subject, otherwise, you can order the data using:
[M,Y,ni] = sortData(M,1,Y,sID);
where Y is the cortical thickness data matrix that you read with
fs_read_Y. Please take a look at the help of sortData. Note that
matrix M only have two columns and you need to build your design
matrix from it. In your case it is quite simple:
X = [ones(length(M),1) M M(:,1).*M(:,2)];
That is to say X contains a column of 1s (the intercept), a column
with the time covariate, a column with the group membership and a
column with the interaction term.
Now, you are ready for fitting the lme model:
stats = lme_mass_fit_vw(X,1,Y,ni,cortex);
The 1 here (second input) means that you are using a single random
effect for the intercept term which is located in column 1 of X. Then
you can test the interaction term using:
CM.C = [0 0 0 1];
F_stats = lme_mass_F(stats,CM);
and write the significance map for visualization and FDR correction in
tksurfer
fs_write_fstats(F_stats,mri,'sig.mgh','sig');
It must be recognized that some basic Matlab knowledge is required to
apply the lme tools. But the gain in flexibility for building your
design matrix and analysis is significant. As you see, the relatively
difficult part is how to get from the Qdec variable to your design
matrix X. It requires some study-specific Matlab code. Sorry, but this
is what he have at this point.
Best
-Jorge
__
De: Alex Hanganu al.hang...@yahoo.ca
Para: FS Mailing List Freesurfer@nmr.mgh.harvard.edu; Jorge
Luis Bernal-Russiel jbernal0...@yahoo.es
Enviado: Miércoles 5 de
Re: [Freesurfer] Hippocampus volume
Hi again, like I said in my previous emails, the measurements from the subfield tools are based on .5x.5x.5 voxels, so you have to divide them by 8 to convert them to cubic milliliters. Then, if you add up the volumes from the subfields (without including the hippocampal fissure), you should get something close to the measurement based on aseg.mgz (2166). Kind regards, Eugenio On Thu, December 6, 2012 10:41 am, Antonella Kis wrote: Dear FS team, After I ran the recon-all to get the total cortical thickness, the volume of the left hypocampus ( = the number of voxels) equals to 2166 which I thought should be the total hippocampal volume. But if we add all the voxel numbers from the hippocampal subfield I will get a much larger number so I wonder which one represents the true total volume in terms of number of voxels. Can you also please advise how can I get differentiated hipocampus segmentation in form of head and body. Thank you. Antonella___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] mri_glmfit-sim for interhemispheric comparison
Hi Doug, I did surface-based inter-hemispheric comparison. I used an arbitrary surface data (.mgz) resampled from a volume data (.nii), otherwise I follow the instruction. http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi I got a good result for mri_glmfit. But when I run mri_glmfit-sim, the following error messeage popped up. ERROR: cannot find $FRESURFER_HOME/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/abs/th2 0/mc-z.csd I did not find fwhm00anywhere in the downloaded file mult-comp-cor, although I found fwhm01-30 directories. Am I missing somethine? Thank you very much in advance, Shige ___ 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] question retinotopic mapping
Julia, what version of FS are you using? It looks like pre-5.0. Can you upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it is becoming increasingly hard to support version 4. doug On 12/06/2012 02:45 AM, Julia Foecker wrote: thanks. attached the info file. When I run the surf-sess command after that, it shows the functional on a surface (see attached but the values at the occip regions show inf. (see figure 1 attached). Moreover, when I try to load the occipital patch it shows me the attached file (fig.3) and I cannot use the command - configure - overlay to change settings. I have used fake ecc. runs (I have recorded only polar runs). Would you have any further suggestions? Thanks, Julia On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote It should automatically detect that this was a retinotopy analysis and then load the polar and eccen. Was this configured as a retinotopy analysis? Can you send me the $ANALYSIS_PHASE/analysis.info file? doug On 12/05/2012 04:12 PM, Julia Foecker wrote: Hi Doug, I tried now several ways to get the maps on the surface: 1. When I am deleting -retinotopy flag and type in: tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE I got the message:no contrast has been specified (I do not have any contrasts in the analysis, just use polar angle maps) 2. I tried to use the commands on the website you referred to, but I do not have -surface in the preproc-sess (see attached) The other commands depend on this preproc-sess command. 3. I tried the following command paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE and I got the errors listed below... I am not sure how to procede. Would you have any further suggestions? Many thanks, Julia Thanks, Julia 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. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_glmfit-sim for interhemispheric comparison
Shige, it is looking for tables of cluster p-values (the csd files). When you followed the wiki instructions, did you tell it to use fsaverage_sym as the target subject? You must have used a subject called average. doug On 12/06/2012 11:53 AM, Shigetoshi Takaya wrote: Hi Doug, I did surface-based inter-hemispheric comparison. I used an arbitrary surface data (.mgz) resampled from a volume data (.nii), otherwise I follow the instruction. http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi I got a good result for mri_glmfit. But when I run mri_glmfit-sim, the following error messeage popped up. ERROR: cannot find $FRESURFER_HOME/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/abs/th20/mc-z.csd I did not find “fwhm00”anywhere in the downloaded file “mult-comp-cor”, although I found fwhm01-30 directories. Am I missing somethine? Thank you very much in advance, Shige -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Running recon-all on a series of scans
Hi Natasha, yes, you have to run recon-all separately for each scan. doug On 12/06/2012 11:14 AM, Natasha Jawa wrote: Hi, Is it possible to run recon-all on a series of scans? I have multiple scans that I want to process longitudinally. The .nii files have all been converted to .mgz files and labelled sequentially (i.e., 001.mgz, 002.mgz, etc.) in /Applications/freesurfer/subjects/subjid/mri. I've tried running recon-all on this whole folder with the command line: recon-all -subjid subjid -all, but it does not execute properly. Do I have to run each of these scans separately using recon-all (i.e., do I need to use a separate terminal for each scan)? Thank you in advance for your time and help. ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] image flip after use of mri_vol2surf/mri_surf2vol
Hi Hubert, The physical side of the image in fslview is not indicative of the actual side. You have to look at the little letters on the side to see what side it is actually on. When you do this, do you see an R or an L? BTW, you might want to use mris_volsmooth which was written to do this kind of thing. Also, I would not use the .w file format. That format is pretty old and does not support multiple frames. Just use mgh format. doug On 12/05/2012 05:40 PM, Fonteijn, H.M.J. (H.) wrote: Hello, I'm relatively new to Freesurfer so chances are that this is a pretty basic error on my side but here goes anyhow. I'm trying to use mri_vol2surf for surface-based smoothing of functional MRI data. I would then like to extract time courses from the surface with spm functions by converting the surface to a volume again with mri_surf2vol. Specifically the commands I'm using are: bbregister --s subject0016 --mov volume0001.nii.gz --reg epi2T1.dat --init-spm --bold mri_vol2surf --mov volume0001.nii.gz --reg epi2T1.dat --surf-fwhm 8 --hemi lh --projdist-avg 0 1 0.1 --o ./volume0001Surf_lh.w --out_type paint mri_surf2vol --surfval volume0001Surf_lh.w paint --hemi lh --projfrac 0.5 --reg epi2T1.dat --o volume0001Surf2Vol_lh.nii --template volume0001.nii.gz Registration looks allright with tkregister2. I'm only using one volume (volume0001.nii.gz) to test this set of commands. However if I now view volume0001Surf2Vol_lh.nii in fslview, it shows the hemisphere on the right. I'm pretty sure that this is actually the left hemisphere but now flipped. I wonder how this can be solved. All the best, Hubert ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] how is fsnr computed?
freesurfers, i've been using my own scripts to compute tSNR for data i was running through FSL, but i'm now running the data through freesurfer and i wanted to better understand what the fsnr volumes spit out by selxavg3-sess are. i poked around the wiki and mailing archives and couldn't find answers to the following questions: 1. how is fsnr computed? tsnr is mean_of_vox_time_course/std_of_vox_time_course -- is fsnr the same thing with a different name? 2. what kind of preprocessing is done on the data before fsnr is computed? since freesurfer removes linear trends at the modeling stage, not the preprocessing stage, are linear trends removed from the data going into fsnr calculations? is anything else regressed out before fsnr is computed (e.g., other nuisance regressors)? 3. what's the difference between raw.fsnr.nii.gz, fsnr.nii.gz, and fsnr2.nii.gz? 4. is fsnr.dat the mean in the whole brain mask (i.e., gm and wm)? separately, random other question: what are the h.dat, h.nii.gz, and h-offset.nii.gz file/volumes? thanks in advance! alex kell ___ 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] how is fsnr computed?
Hi Alex, On 12/06/2012 12:21 PM, Alex Kell wrote: freesurfers, i've been using my own scripts to compute tSNR for data i was running through FSL, but i'm now running the data through freesurfer and i wanted to better understand what the fsnr volumes spit out by selxavg3-sess are. i poked around the wiki and mailing archives and couldn't find answers to the following questions: 1. how is fsnr computed? tsnr is mean_of_vox_time_course/std_of_vox_time_course -- is fsnr the same thing with a different name? Pretty close, though maybe a little different. It is the offset/std_of_residuals. This all happens after the model is fit. The offset here is close to the mean but technically it is the regression coefficient of the regressor of all 1s. After the full model is fit, the estimated time course is subtracted from the actual time course to give the residuals. So this is the Function SNR after removing task signal and nuisance regressors. 2. what kind of preprocessing is done on the data before fsnr is computed? since freesurfer removes linear trends at the modeling stage, not the preprocessing stage, are linear trends removed from the data going into fsnr calculations? is anything else regressed out before fsnr is computed (e.g., other nuisance regressors)? The full model is regressed out. 3. what's the difference between raw.fsnr.nii.gz, fsnr.nii.gz, and fsnr2.nii.gz? The raw fsnr does not regress out anything just mean/std 4. is fsnr.dat the mean in the whole brain mask (i.e., gm and wm)? Yes separately, random other question: what are the h.dat, h.nii.gz, and h-offset.nii.gz file/volumes? these are somewhat redundant with the beta volume. In the pre-5.0 version, these were the only files produced. They are created for compatibility with some of the older tools. doug thanks in advance! alex kell ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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_glmfit-sim for interhemispheric comparison
Thanks for your reply, Doug After inter-hemispheric registration onto fsaverage_sym using surfreg, I did not use mris_preproc in my analysis because of the following two reasons: (i) I thought I can't use --meas because the input is an arbitrary surface data. (ii) I don't want to use --paired-diff because I don't want the input pruned before taking the difference. Instead, I took the following steps: (1) resample the data onto fsaverage_sym using mri_surf2surf (2) take the difference in each subject using fscalc $fscalc lh.lh_subj1.mgz -sub lh.rh_subj1.mgz --o lh.lh-rh_subj1.mgz (3) concatenate the subjects together $mri_concat lh-rh_subj1 lh-rh_subj2 --o (4) smooth (mris_fwhm) and analyze (mri_glmfit). Are these steps not good for mri_glmfit-sim? Best, Shige -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, December 06, 2012 11:59 AM To: Shigetoshi Takaya Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mri_glmfit-sim for interhemispheric comparison Shige, it is looking for tables of cluster p-values (the csd files). When you followed the wiki instructions, did you tell it to use fsaverage_sym as the target subject? You must have used a subject called average. doug On 12/06/2012 11:53 AM, Shigetoshi Takaya wrote: Hi Doug, I did surface-based inter-hemispheric comparison. I used an arbitrary surface data (.mgz) resampled from a volume data (.nii), otherwise I follow the instruction. http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi I got a good result for mri_glmfit. But when I run mri_glmfit-sim, the following error messeage popped up. ERROR: cannot find $FRESURFER_HOME/average/mult-comp-cor/fsaverage_sym/lh/cortex/fwhm00/a bs/th20/mc-z.csd I did not find fwhm00anywhere in the downloaded file mult-comp-cor, although I found fwhm01-30 directories. Am I missing somethine? Thank you very much in advance, Shige -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] question retinotopic mapping
The problem is that you have a version 4 analysis that you are trying to view with version 5 tools. To use version 5 visualization, you'll need to remake the analysis in version 5 and then reanalyze. Otherwise, you'll have to use the version 4 stream (instructions attached). It is somewhat difficult for me to support the version 4 stream because it is so old. doug On 12/06/2012 03:27 PM, Julia Foecker wrote: I have the two versions 4 and 5 , but I am receiving the same error messages with 5.1 For example when I type in preproc-see there is no -surface as well. Isn't there any other possibility to solve that issue? It may have also sth. to do with the computer. I have a new Mac, not sure if this may be the reason. As I said, I do not think this is due to the version...I just tried that and similar requirements are missing when I am doing that with 5.1 Thanks again for further advices, Julia On 12/6/12 11:56 AM, Douglas N Greve wrote: Julia, what version of FS are you using? It looks like pre-5.0. Can you upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it is becoming increasingly hard to support version 4. doug On 12/06/2012 02:45 AM, Julia Foecker wrote: thanks. attached the info file. When I run the surf-sess command after that, it shows the functional on a surface (see attached but the values at the occip regions show inf. (see figure 1 attached). Moreover, when I try to load the occipital patch it shows me the attached file (fig.3) and I cannot use the command - configure - overlay to change settings. I have used fake ecc. runs (I have recorded only polar runs). Would you have any further suggestions? Thanks, Julia On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote It should automatically detect that this was a retinotopy analysis and then load the polar and eccen. Was this configured as a retinotopy analysis? Can you send me the $ANALYSIS_PHASE/analysis.info file? doug On 12/05/2012 04:12 PM, Julia Foecker wrote: Hi Doug, I tried now several ways to get the maps on the surface: 1. When I am deleting -retinotopy flag and type in: tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE I got the message:no contrast has been specified (I do not have any contrasts in the analysis, just use polar angle maps) 2. I tried to use the commands on the website you referred to, but I do not have -surface in the preproc-sess (see attached) The other commands depend on this preproc-sess command. 3. I tried the following command paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE and I got the errors listed below... I am not sure how to procede. Would you have any further suggestions? Many thanks, Julia Thanks, Julia 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. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Retinotopy analysis in FS-FAST For each session, create retinotopy paradigm files in each of the run directories. These paradigm files are different than an event-related or block paradigm (which list which stimulus was presented when). A retinotopy paradigm file has information about whether the run was an eccentricity or polar stimulus and in what direction the stimulus was presented. For polar, the direction is indicates whether the spoke was traveling clockwise or counter-clockwise. For eccen, the direction is indicates whether the ring was expanding or contracting. The definition of what's positive and what's negative is arbitrary, though it must be consistent. If you don't have both directions, just use positive. For example, if there were four runs (001, 002, 003, 004), two eccen and two polar, both in the positive and negative directions. Create a file (eg, rtopy.par) in each run. Assuming run 001 was eccen in the negative direction, then the rtopy.par for run 001 would look like: cut here stimtype eccen direction neg cut here If needed, create a run-list file with the all retinotopy runs (regardless of whether it was eccen or polar). Create the analysis: mkanalysis-sess \ -a rtopy \ -TR 2 \ -designtype retinotopy \ -paradigm rtopy.par \ -funcstem fmcsm5 \ -ncycles 8 Preprocess preproc-sess -s avdk -fwhm 8 Run the
[Freesurfer] update mri_glmfit
Hi I saw an updated version of mri_glmfit in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/. Should I update this file in my freesurfer installation. What do this fix? Is is not in the release notes? Knut J ___ 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] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?
How can I get 300 dpi resolution or about when saving tiff files in tksurfer? ___ 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] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?
Hi Knut the tiffs written by tksurfer are 600x600 regardless of what DPI you set. You can change the dpi with convert (or photoshop), but it won't change the # of pixels. cheers Bruce On Thu, 6 Dec 2012, Knut J Bjuland wrote: How can I get 300 dpi resolution or about when saving tiff files in tksurfer? ___ 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] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?
Perhaps you can maximize the tksurfer window on a large monitor, take a whole screen screenshot, and then in a photo editing program: decrease the physical size of the image (in mm or inches) while not decreasing the matrix size. You can do this in photoshop in Image Image Size And then change the document size until the resolution is 300. This will increase the DPI to make nice figures. What Bruce suggests will just upsample the image (without adding detail), which is not what journals have in mind when they ask for 300dpi figures. Keep in mind that the document size is the printable size, so your image will get smaller on the printed page when you do this. Often, figures have multiple panels and if you take each panel as a full screen image on a large monitor and then reduce the size you will have more than 300dpi to spare in the end result. Peace, Matt. On 12/6/12 3:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Knut the tiffs written by tksurfer are 600x600 regardless of what DPI you set. You can change the dpi with convert (or photoshop), but it won't change the # of pixels. cheers Bruce On Thu, 6 Dec 2012, Knut J Bjuland wrote: How can I get 300 dpi resolution or about when saving tiff files in tksurfer? ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Longitudinal analysis - contrast
Hello Martin,
Thanks for your confirmation. I downloaded the last version of
FreeSurfer: the dev5-20120624, from the ..fswiki/LMEModels page, but
there is the old mris_preproc, so I will use the fsgd file.
Thanks for pointing out about the long.base - files!! That was a mistake
of mine. And thanks for the shell command line !
So the fsgd file was created /only/ with long subjects, then I created
the lh.thickness_sm10.mgh file and went further ! OK.
===
Hi Jorge,
Thanks for showing clearly the steps ! Everything went fine. The X
contains those columns as you said.
our stats command is:
/stats = lme_mass_fit_vw(X,1,Y,144,cortex);
/where 144 is the 2*ones. We have 36 subjects and 2 time points, so we
have 72 ones * 2 - 144. (but I also tried with 72, 36, 2)
Unfortunately, there is again an error:
/File: lme_mass_fit.m Line: 162 Column: 14//
//The variable stats in a parfor cannot be classified.
Error in == lme_mass_fit_vw at 73
[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
/
Also when applying:
/[M,Y,144] = sortData(M,1,Y,sID);
/there is an error:/An array for multiple LHS assignment cannot contain
numeric value.
/Our M contains: 72x2 double value
The X: 72x4 double value
but the sID contains: 73x1 cell
so we thought that might be the problem and we removed the cell sID ,
and we got and sID: 72x1 cell. The error persisted.
did we miss something ?
Thank you !
Sincerely,
Alex.
Le 06/12/2012 11:15 AM, Martin Reuter a écrit :
Yes,
in 5.2 there should be the two new options --qdec and --qdec-long
to allow passing qdec tables both in the regular cross sectional and in
the longitudinal format in addition to the existing other ways of
passing subjects lists (--s or --fsgd or --f ).
Now care needs to be taken in the longitudinal setting. What you want is
to get the files (e.g. thickness) from the *.long.base directories
into the target (e.g fsaverage space). Not from the cross sectional
directories!
For this you will be able to use the longitudinal qdec file (with a
column of 'fsid' and 'fsid-base' to group time points into subjects, see
wiki).
In 5.1 you should do the following:
create a text file with each longitudinal id (containing
the .long.base ) per line and pass it using the --f flag.
So in the example below you'd write:
002.long.002_base
003.long.003_base
003_m6.long.003_base
You can use a simple shell command to get such a list from a
longitudinal qdec file:
cat long.qdec.table.txt | awk '{if ($1 != fsid substr($1,0,1) !=
#) printf(%s.long.%s\n, $1, $2)}' outsubjectsfile.txt
Then preproc will do its job. The order of subjects needs to be
identical to the qdec file that you use to run the LME matlab tools to
ensure thickenss maps are stacked in the same order as you pass the
covariates.
Best, Martin
On Thu, 2012-12-06 at 04:27 +, jorge luis wrote:
Hi Alex
I think that Martin added the flag --qdec to mris_preproc for version
5.2. Martin, could you confirm this please?
The code for building the study design matrix X that is in the wiki is
just an example of how lme tools can be used for that purpose but the
actual instance of your code will depend on your particular Qdec
table. For instance, usually, Freesurfer's longitudinal Qdec tables
are of the form:
fsidfsid-base sIDtime group...
002002_base 0020 0
003003_base0030 1
003_m6003_base0030.56 1
003_m12 003_base0031.121
003_m24 003_base0032.2 1
005005_base00500
005_m6005_base0050.45 0
005_m12 005_base 0051.2 0
were fsid is the Freesurfer's ID, fsid-base is the name of the
subject's specific template, sID is the subject-specific ID uniquely
identifying each subject, time is the time covariate and group is
the group membership covariate (there can be more covariates of
course). I suppose that you processed your longitudinal MRI scans
using a Qdec table similar to that.
You can read that Qdec table into Matlab:
Qdec = fReadQdec('qdec.table.dat');
Now you need to build your numeric design matrix X from the cell
string array Qdec to represent a specific longitudinal design. Here
you don't need the columns fsid and fsid-base in Qdec so you simply
remove them:
Qdec = rmQdecCol(Qdec,1);
Qdec = rmQdecCol(Qdec,1);
The you can grab the subject-specific ID:
sID = Qdec(:,1);
and then remove that column:
Qdec = rmQdecCol(Qdec,1);
You can now convert your cell string array Qdec to a numeric matrix:
M = Qdec2num(Qdec);
Here, the data in M is already ordered according to time for each
subject, otherwise, you can order the data using:
[M,Y,ni] = sortData(M,1,Y,sID);
where Y is the cortical thickness data matrix that you read with
fs_read_Y. Please take a look at the help of sortData. Note that
matrix M only have two columns and you need to build your design
matrix from it. In your case it
Re: [Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?
If you want to get a figure with arbitrarily high resolution regardless of the screen size, have a look at PySurfer*. It's not an official part of freesurfer but can display many of the freesurfer files. It can produce high resolution figures by moving the camera, taking screenshots and then assembling them. *http://pysurfer.github.com/index.html Best, Martin On 12/06/12 16:40, Matt Glasser wrote: Perhaps you can maximize the tksurfer window on a large monitor, take a whole screen screenshot, and then in a photo editing program: decrease the physical size of the image (in mm or inches) while not decreasing the matrix size. You can do this in photoshop in Image Image Size And then change the document size until the resolution is 300. This will increase the DPI to make nice figures. What Bruce suggests will just upsample the image (without adding detail), which is not what journals have in mind when they ask for 300dpi figures. Keep in mind that the document size is the printable size, so your image will get smaller on the printed page when you do this. Often, figures have multiple panels and if you take each panel as a full screen image on a large monitor and then reduce the size you will have more than 300dpi to spare in the end result. Peace, Matt. On 12/6/12 3:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Knut the tiffs written by tksurfer are 600x600 regardless of what DPI you set. You can change the dpi with convert (or photoshop), but it won't change the # of pixels. cheers Bruce On Thu, 6 Dec 2012, Knut J Bjuland wrote: How can I get 300 dpi resolution or about when saving tiff files in tksurfer? ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Luessi, Ph.D. Research Fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 Fax: +1 617 726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] winkler surf data with qdec ?
Hi , I have winkler variety surface area data that is already smoothed and converted to vertex wise data on my average subject. Each subject has a file rh.ico7.fwhm10.mgh, lh... and Doug gave me a way with mri_concat to assemble the data into a single file so i can run command line mri_glmfit type analysis and that worked out fine. I would like if i can to use qdec so our non command line unix oriented postdoc could easily run a lot of models of interest. the LGI page says you can do recon-all -s my_subject_id -qcache -measure pial_lgi and then add a file .Qdecrc with MEASURE1 = pial_lgi but recon-all -qcache will do smoothing and smoothing has already been done by his fancy specially designed method for the surface interpolated data and also my data is in .mgh format and not curv format like thickness or lgi. is there a way i can cook this goose ? thanks 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] Longitudinal analysis - contrast
Hi Alex
Sorry, my bad. You are right. To grab the subjects'ID the correct code is:
sID = Qdec(2:end,1);
I'm going to fix that in the wiki. The new error is due to the numeric value on
the left hand side of
[M,Y,144] = sortData(M,1,Y,sID);
You cannot assign any value to 144. Just change that code by this:
[M,Y,ni] = sortData(M,1,Y,sID);
and use ni instead of 144 everywhere. Note that ni must be a vector of the
same size as the number of subjects in your study (36), not a single numeric
value.
Best
-Jorge
De: Alex Hanganu al.hang...@yahoo.ca
Para: Martin Reuter mreu...@nmr.mgh.harvard.edu
CC: FS Mailing List Freesurfer@nmr.mgh.harvard.edu; Jorge Luis Bernal-Rusiel
jbernal0...@yahoo.es
Enviado: Jueves 6 de diciembre de 2012 16:45
Asunto: Re: Re: [Freesurfer] Longitudinal analysis - contrast
Hello Martin,
Thanks for your confirmation. I downloaded the last version of
FreeSurfer: the dev5-20120624, from the ..fswiki/LMEModels page,
but there is the old mris_preproc, so I will use the fsgd file.
Thanks for pointing out about the long.base - files!! That was a
mistake of mine. And thanks for the shell command line !
So the fsgd file was created only with long subjects, then I created the
lh.thickness_sm10.mgh file and went further ! OK.
===
Hi Jorge,
Thanks for showing clearly the steps ! Everything went fine. The X
contains those columns as you said.
our stats command is:
stats = lme_mass_fit_vw(X,1,Y,144,cortex);
where 144 is the 2*ones. We have 36 subjects and 2 time points, so we have
72 ones * 2 - 144. (but I also tried with 72, 36, 2)
Unfortunately, there is again an error:
File: lme_mass_fit.m Line: 162 Column: 14
The variable stats in a parfor cannot be classified.
Error in == lme_mass_fit_vw at 73
[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
Also when applying:
[M,Y,144] = sortData(M,1,Y,sID);
there is an error:An array for multiple LHS assignment cannot contain numeric
value.
Our M contains: 72x2 double value
The X: 72x4 double value
but the sID contains: 73x1 cell
so we thought that might be the problem and we removed the cell
sID , and we got and sID: 72x1 cell. The error
persisted.
did we miss something ?
Thank you !
Sincerely,
Alex.
Le 06/12/2012 11:15 AM, Martin Reuter a écrit :
Yes, in 5.2 there should be the two new options --qdec and --qdec-long to
allow passing qdec tables both in the regular cross sectional and in
the longitudinal format in addition to the existing other ways of
passing subjects lists (--s or --fsgd or --f ). Now care needs to be taken in
the longitudinal setting. What you want is
to get the files (e.g. thickness) from the *.long.base directories
into the target (e.g fsaverage space). Not from the cross sectional
directories! For this you will be able to use the longitudinal qdec file (with a
column of 'fsid' and 'fsid-base' to group time points into subjects, see
wiki). In 5.1 you should do the following:
create a text file with each longitudinal id (containing
the .long.base ) per line and pass it using the --f flag.
So in the example below you'd write:
002.long.002_base
003.long.003_base
003_m6.long.003_base You can use a simple shell command to get such a list from
a
longitudinal qdec file:
cat long.qdec.table.txt | awk '{if ($1 != fsid substr($1,0,1) !=
#) printf(%s.long.%s\n, $1, $2)}' outsubjectsfile.txt Then preproc will
do its job. The order of subjects needs to be
identical to the qdec file that you use to run the LME matlab tools to
ensure thickenss maps are stacked in the same order as you pass the
covariates. Best, Martin On Thu, 2012-12-06 at 04:27 +, jorge luis wrote:
Hi Alex I think that Martin added the flag --qdec to mris_preproc for version
5.2. Martin, could you confirm this please? The code for building the study
design matrix X that is in the wiki is
just an example of how lme tools can be used for that purpose but the
actual instance of your code will depend on your particular Qdec
table. For instance, usually, Freesurfer's longitudinal Qdec tables
are of the form: fsidfsid-base sIDtime group...
002002_base 0020 0
003003_base0030 1
003_m6003_base0030.56 1
003_m12 003_base0031.121
003_m24 003_base0032.2 1
005005_base00500
005_m6005_base0050.45 0
005_m12 005_base 0051.2 0 were “fsid” is the Freesurfer's ID,
“fsid-base” is the name of the
subject's specific template, sID is the subject-specific ID uniquely
identifying each subject, “time” is the time covariate and group is
the group membership covariate (there can be more covariates of
course). I suppose that you processed your longitudinal MRI scans
using a Qdec table similar to that. You can read that Qdec table into Matlab:
Qdec =
[Freesurfer] De-trending resting state data
I'm working with raw timeseries waveform data from a resting state dataset. There's one run per participant, so no between-run normalization is required. With Doug's help, I have mastered extracting the timeseries information from individual ROIs in surface space. The timeseries data is the product of the preproc-sess script, to which I additionally added the -inorm parameter to extract the mean timeseries for the entire volume. One concern I had was that correlations between timeseries from different ROIs might be artificially inflated by scanner drift. For example, if the overall signal increases or decreases as a function of time over the course of the run or fluctuates periodically, then for any two regions, their signals will go up or down together as a result. This should in turn make the timeseries from these two regions more correlated. I have no strong evidence that scanner drift is a particular problem in my dataset, but it seems likely enough in a 6 minute run that I want to mitigate the problem. I can't really put these data through selxavg, as I do not have a model to fit for resting state data, and in any case would like to work with the timeseries itself, rather than residuals or any other by-product of an HRF model. I was wondering if simply subtracting the global mean signal waveform from each ROI waveform would be a reasonable strategy for removing drift, or if there are any standalone commands that are called by some of the super-scripts that I can use without carrying out a first level analysis. Thanks, Chris ___ 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] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?
Hi Bruce, Do you upsample the tiffs from tksurfer when making image for publications? Or do you use another program in FreeSurfer suite? Knut J On 12/06/2012 10:22 PM, Bruce Fischl wrote: Hi Knut the tiffs written by tksurfer are 600x600 regardless of what DPI you set. You can change the dpi with convert (or photoshop), but it won't change the # of pixels. cheers Bruce On Thu, 6 Dec 2012, Knut J Bjuland wrote: How can I get 300 dpi resolution or about when saving tiff files in tksurfer? ___ 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
