Re: [Freesurfer] Problem with Longitudinal QDEC file and mris_preproc
Hi Martin, Thank you for your help and clarifications. I did run the *_to_table commands and now my LME analyses are running smoothly. Best, Jennifer Legault On Mon, Mar 9, 2015 at 11:35 AM, Martin Reuter wrote: > Hi Jennifer, > > if you are interested in volumes from the stats file, you need to use > aseg_stats_to_table and aparc_stats… to stack those data across subjects and > time points into a single table that you then analyze with the LME tools. > mris_preproc is only for stacking surface maps. > > The longitudinal QDEC file can be the same, you only need it to tell > aseg_stats_2_table etc how to create the file names for the individual > *.long.* directories. So that file only needs 2 columns (fsid, fsid-base ) > for that. And maybe you want to pass other covariates (e.g. time from > baseline, average age, gender etc) into LME via that same qdec table. The FS > stats (e.g. either thickness maps, or stats tables) will be read separately. > > If you still have difficulties with the long QDEC file, try using space > separated instead of tab! > > You don’t smooth the volume data. Look at the *_to_table commands to > generate the tables. > > Best, Martin > > > On Mar 6, 2015, at 5:09 PM, Jennifer Legault wrote: > > Hi all, > > > I am new to Freesurfer and have run my participants’ data through the > longitudinal preprocessing stream and am now trying to assemble my data so > that they can be put into a linear mixed effect model analysis. While the > longitudinal tutorial with cortical thickness data is very helpful, I am > interested in GM volume (specific ROIs in aseg. + the lh and rh aparc. > files) and have run into a few problems. > > > 1) Problem with mris_preproc command/with QDEC file: > > > a) I have made a Longitudinal QDEC file (attached in this comment as an > excel file and .dat file) and I made sure to export to my Subjects dir, and > then put in the following command: > > mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi > lh --meas volume --out lh.volume.mgh > > When I run this command, it only runs for my first participant (which it > takes from the Longitudinal QDEC file, such that if I take out the first row > of the QDEC file, it starts with the next participant) > > I do not receive any sort of error message or anything, it just doesn’t keep > running. Furthermore, I cannot find the output file (lh.volume.mgh) > anywhere in my subjects directory. > > b) I am also wondering whether I need to make separate QDEC files for 1) > aseg data 2) lh.aparc and 3) rh.aparc. Right now, my QDEC file has all of > the information of interest in one place. > > c) I made the QDEC file in excel, and saved it as tab delimited (when I try > to save it as space delimited (.prn--which I rename as .dat) and re-open it, > it loses many of my headers and data). Does it have to be space delimited, > and if so, is there another way of formatting it as space delimited? If > not, then is there something else wrong with my QDEC format? > > > 2) I do not know whether I am supposed to smooth the volume stack. > > According to my understanding of the Longitudinal tutorial, we should first > run mris_preproc to concatenate our files and resample volume data to a > common subject. Next, we should smooth the stacked/concatenated file. > Should I use the following command: > > mri_vol2surf --src input file --hemi hemisphere --fwhm 10 --out outpufile > > > Thank you for taking the time to read this email, I sincerely appreciate it. > > > Best, > > Jennifer Legault > Ph.D candidate, Neuroscience > Brain, Language, and Computation Lab > The Pennsylvania State University > > > -- > Jennifer Legault > Ph.D candidate, Neuroscience > Brain, Language, and Computation Lab > The Pennsylvania State University > ___ > 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. > -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with Longitudinal QDEC file and mris_preproc
Hi Jennifer, if you are interested in volumes from the stats file, you need to use aseg_stats_to_table and aparc_stats… to stack those data across subjects and time points into a single table that you then analyze with the LME tools. mris_preproc is only for stacking surface maps. The longitudinal QDEC file can be the same, you only need it to tell aseg_stats_2_table etc how to create the file names for the individual *.long.* directories. So that file only needs 2 columns (fsid, fsid-base ) for that. And maybe you want to pass other covariates (e.g. time from baseline, average age, gender etc) into LME via that same qdec table. The FS stats (e.g. either thickness maps, or stats tables) will be read separately. If you still have difficulties with the long QDEC file, try using space separated instead of tab! You don’t smooth the volume data. Look at the *_to_table commands to generate the tables. Best, Martin > On Mar 6, 2015, at 5:09 PM, Jennifer Legault wrote: > > Hi all, > > > > I am new to Freesurfer and have run my participants’ data through the > longitudinal preprocessing stream and am now trying to assemble my data so > that they can be put into a linear mixed effect model analysis. While the > longitudinal tutorial with cortical thickness data is very helpful, I am > interested in GM volume (specific ROIs in aseg. + the lh and rh aparc. files) > and have run into a few problems. > > > > 1) Problem with mris_preproc command/with QDEC file: > > > > a) I have made a Longitudinal QDEC file (attached in this comment as an excel > file and .dat file) and I made sure to export to my Subjects dir, and then > put in the following command: > > mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh > --meas volume --out lh.volume.mgh > > When I run this command, it only runs for my first participant (which it > takes from the Longitudinal QDEC file, such that if I take out the first row > of the QDEC file, it starts with the next participant) > > I do not receive any sort of error message or anything, it just doesn’t keep > running. Furthermore, I cannot find the output file (lh.volume.mgh) anywhere > in my subjects directory. > > b) I am also wondering whether I need to make separate QDEC files for 1) aseg > data 2) lh.aparc and 3) rh.aparc. Right now, my QDEC file has all of the > information of interest in one place. > > c) I made the QDEC file in excel, and saved it as tab delimited (when I try > to save it as space delimited (.prn--which I rename as .dat) and re-open it, > it loses many of my headers and data). Does it have to be space delimited, > and if so, is there another way of formatting it as space delimited? If not, > then is there something else wrong with my QDEC format? > > > > 2) I do not know whether I am supposed to smooth the volume stack. > > According to my understanding of the Longitudinal tutorial, we should first > run mris_preproc to concatenate our files and resample volume data to a > common subject. Next, we should smooth the stacked/concatenated file. > Should I use the following command: > > mri_vol2surf --src input file --hemi hemisphere --fwhm 10 --out outpufile > > > > Thank you for taking the time to read this email, I sincerely appreciate it. > > > > Best, > > Jennifer Legault > Ph.D candidate, Neuroscience > Brain, Language, and Computation Lab > The Pennsylvania State University > > > -- > Jennifer Legault > Ph.D candidate, Neuroscience > Brain, Language, and Computation Lab > The Pennsylvania State University > ___ > 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] Problem with Longitudinal QDEC file and mris_preproc
Hi all, I am new to Freesurfer and have run my participants’ data through the longitudinal preprocessing stream and am now trying to assemble my data so that they can be put into a linear mixed effect model analysis. While the longitudinal tutorial with cortical thickness data is very helpful, I am interested in GM volume (specific ROIs in aseg. + the lh and rh aparc. files) and have run into a few problems. 1) Problem with mris_preproc command/with QDEC file: a) I have made a Longitudinal QDEC file (attached in this comment as an excel file and .dat file) and I made sure to export to my Subjects dir, and then put in the following command: mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh --meas volume --out lh.volume.mgh When I run this command, it only runs for my first participant (which it takes from the Longitudinal QDEC file, such that if I take out the first row of the QDEC file, it starts with the next participant) I do not receive any sort of error message or anything, it just doesn’t keep running. Furthermore, I cannot find the output file (lh.volume.mgh) anywhere in my subjects directory. b) I am also wondering whether I need to make separate QDEC files for 1) aseg data 2) lh.aparc and 3) rh.aparc. Right now, my QDEC file has all of the information of interest in one place. c) I made the QDEC file in excel, and saved it as tab delimited (when I try to save it as space delimited (.prn--which I rename as .dat) and re-open it, it loses many of my headers and data). Does it have to be space delimited, and if so, is there another way of formatting it as space delimited? If not, then is there something else wrong with my QDEC format? 2) I do not know whether I am supposed to smooth the volume stack. According to my understanding of the Longitudinal tutorial, we should first run mris_preproc to concatenate our files and resample volume data to a common subject. Next, we should smooth the stacked/concatenated file. Should I use the following command: mri_vol2surf --src input file --hemi hemisphere --fwhm 10 --out outpufile Thank you for taking the time to read this email, I sincerely appreciate it. Best, Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University long.qdec.table.xlsx Description: MS-Excel 2007 spreadsheet long.qdec.table.dat Description: Binary data ___ 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.
