Hi Doug,
What I mean by "covary for a categorical variable", what I want to do is covary for gender. Sorry for my confusion terminology. Thank you for your help!
Jeff
On Wed, Sep 5, 2012 at 6:00 AM, freesurfer-request@nmr.mgh.harvard.eduwrote:
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Today's Topics:
- Re: Repost: Converting BV ROIs to FS (Bruce Fischl)
- Re: Repost: Converting BV ROIs to FS (Katie Bettencourt)
- Re: freesurfer tutorial data (Help Desk -- Paul Raines)
- Re: creating a skull (Borzello, Mia)
- Re: error in long_mris_slopes command (Martin Reuter)
- mris_anatomical_stats on multiple subjects (Alexandra Tanner)
- Re: freesurfer tutorial data (Dix Meiberth)
- Re: creating a skull (Bruce Fischl)
- Cortical parcellations and probtrackx2 in diffusion space (Alistair Perry)
- Covary for categorical variable in QDEC (Jeff Sadino)
- Re: Repost: Converting BV ROIs to FS (Bruce Fischl)
- Re: repeated measures ANOVA with two groups (Douglas N Greve)
- Re: freesurfer tutorial data (Help Desk -- Paul Raines)
- Re: missing ROI when using mri_label2vol to transfer ic2.tri (Douglas N Greve)
- Re: Freesurfer-Error message (Varghese Chikku)
- Re: Freesurfer-Error message (Bruce Fischl)
- Re: FDR Correction of NHP Surface Data (Douglas N Greve)
- Re: mri_watershed and other errors. (Darren Gitelman)
- Re: resending question about 3rd level analysis (Douglas N Greve)
- Re: mris_anatomical_stats on multiple subjects (Alexandra Tanner)
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Katie Bettencourt kcb@wjh.harvard.edu Cc: freesurfer maillist freesurfer@nmr.mgh.harvard.edu Date: Tue, 4 Sep 2012 12:24:09 -0400 (EDT) Subject: Re: [Freesurfer] Repost: Converting BV ROIs to FS Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do?
sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote:
So our lab is running a couple analyses and we are gettingdifferent results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated.
Katie
---------- Forwarded message ---------- From: Katie Bettencourt kcb@wjh.harvard.edu To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: freesurfer maillist freesurfer@nmr.mgh.harvard.edu Date: Tue, 4 Sep 2012 13:18:42 -0400 Subject: Re: [Freesurfer] Repost: Converting BV ROIs to FS Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different.
Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot?
Katie
On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do?
sorry, Bruce
On Tue, 4 Sep 2012, Katie Bettencourt wrote:
So our lab is running a couple analyses and we are gettingdifferent results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated.
Katie
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/**compliancelinehttp://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.
---------- Forwarded message ---------- From: Help Desk -- Paul Raines help@nmr.mgh.harvard.edu To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu, Dix.Meiberth@ukb.uni-bonn.de Date: Tue, 4 Sep 2012 14:56:22 -0400 (EDT) Subject: Re: [Freesurfer] freesurfer tutorial data 2GB sounds like you reaching maybe a file size limit of your operating system if it is really old. Or if you have are trying to download to a FAT formated external USB drive or such.
-- Paul Raines (http://help.nmr.mgh.harvard.**eduhttp://help.nmr.mgh.harvard.edu )
On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote:
Hi Dix,
not sure what's going on. Have you tried multiple times?
Bruce
On Mon, 3 Sep 2012, Dix.Meiberth@ukb.uni-bonn.de wrote:
Dear sirs and madames,
unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the "bruckner_data_tutorial_subjs.**tar.gz" I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data?
Best regards,
Dix Meiberth (B.Sc. Neurowissenschaften)
Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn
Tel. 0228-287-16366 Dix.Meiberth@ukb.uni-bonn.de
---------- Forwarded message ---------- From: "Borzello, Mia" MBORZELLO@partners.org To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Date: Tue, 4 Sep 2012 19:15:08 +0000 Subject: Re: [Freesurfer] creating a skull I'm using Unix. Should I try something else?
Thanks, m ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 03, 2012 2:45 PM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull
Hi Mia
what platform are you running on?
Bruce On Fri, 31 Aug 2012, Borzello, Mia wrote:
I've been referred to the following link on the freesurfer site to
handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html
thanks, m ________________________________________ From: Louis Nicholas Vinke [vinke@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull
Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis
On Fri, 31 Aug 2012, Borzello, Mia wrote:
Hi freesurfer family,
I am trying to create the inner skull boundary and ran: mri_watershed
-atlas - surf -useSRAS mri.nii brain
However, after it finished running it said it was saving "brain", but
"brain" was an unknown file type. Am i supposed to specify that somewhere?
Thanks in advance, m
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
---------- Forwarded message ---------- From: Martin Reuter mreuter@nmr.mgh.harvard.edu To: Shannon Kogachi skogachi@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Date: Tue, 04 Sep 2012 15:57:21 -0400 Subject: Re: [Freesurfer] error in long_mris_slopes command Hi Shannon,
I have no idea why it would run and then when re-running it fails. Are you calling it exactly the same way? Do you have write permissions in those directories. If it prints the command (mris_label_calc) that it is trying to run, can you try to run only that command?
Also you can try the new version from here: http://martinos.org/~mreuter/long (parameters are a little different, e.g. you need to specify the subjects dir with --sd I think and some other flags have changed from out_??? to name_???, as they can also be inputs )
Best, Martin
On Fri, 2012-08-31 at 09:54 -1000, Shannon Kogachi wrote:
Hi Freesurfers, I've just tried to use the long_mris_slopes command on some longitudinal data. I've created my long.qdec.table.dat file. I've run this command before without any problems but I need to re-run it again. This time when I try to re-run it this error pops up:
ERROR 1 : mris_label_calc intersect did not work?
Is there any way to fix this? it also tells me the following:
cp: target 'path/subjectID/lh.long.cortex.label' is not a directory
Please let me know if there is any way to fix this. thank you!!
-Shannon K. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: "Alexandra Tanner" atanner@nmr.mgh.harvard.edu To: "Douglas N Greve" greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Date: Tue, 4 Sep 2012 17:44:25 -0400 (EDT) Subject: [Freesurfer] mris_anatomical_stats on multiple subjects Hi Doug and Freesurfers,
I'm currently working on extracting thickness measurements from an ROI I manually created. I created my ROI label in tksurfer and applied the label to each subject I'd like to extract thickness data from using mri_label2label. I then used the following command to generate a stats file, with the thickness measurement, from my label: mris_anatomical_stats -f something.stats -l something.label subjid ?h (http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit).
This generated a stats file that gave me the average thickness for my ROI in my subject. I was wondering if there is a way to run the same command, but on multiple subjects at once, so as not to have to run this command on each individual subject. Any suggestions would be greatly appreciated!
Best, Alex
---------- Forwarded message ---------- From: Dix Meiberth dix.meiberth@ukb.uni-bonn.de To: Help Desk -- Paul Raines help@nmr.mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Date: Wed, 5 Sep 2012 00:19:50 +0200 Subject: Re: [Freesurfer] freesurfer tutorial data Thx for your responses. But no, I try to copy to my harddrive on my 1 year old Mac. I think for the fith time right now. There should be no limit but I will doublecheck.
Best regards.
Dix
Von meinem iPhone gesendet
Am 04.09.2012 um 20:56 schrieb Help Desk -- Paul Raines < help@nmr.mgh.harvard.edu>:
2GB sounds like you reaching maybe a file size limit of your operating system if it is really old. Or if you have are trying to download to a FAT formated external USB drive or such.
-- Paul Raines (http://help.nmr.mgh.harvard.edu)
On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote:
Hi Dix,
not sure what's going on. Have you tried multiple times?
Bruce
On Mon, 3 Sep 2012, Dix.Meiberth@ukb.uni-bonn.de wrote:
Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for
freesurfer.
The download interrupted at 2 GB within the "bruckner_data_tutorial_subjs.tar.gz" I already did the recon_all process for 90 brains and wanted to
improve my
skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 Dix.Meiberth@ukb.uni-bonn.de
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
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.
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: "Borzello, Mia" MBORZELLO@partners.org Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Date: Tue, 4 Sep 2012 19:35:57 -0400 (EDT) Subject: Re: [Freesurfer] creating a skull no, that should be fine On Tue, 4 Sep 2012, Borzello, Mia wrote:
I'm using Unix. Should I try something else?
Thanks, m ______________________________**__________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, September 03, 2012 2:45 PM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull
Hi Mia
what platform are you running on?
Bruce On Fri, 31 Aug 2012, Borzello, Mia wrote:
I've been referred to the following link on the freesurfer site to
handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/**pipermail/fieldtrip/2012-** January/004679.htmlhttp://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html
thanks, m ______________________________**__________ From: Louis Nicholas Vinke [vinke@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull
Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis
On Fri, 31 Aug 2012, Borzello, Mia wrote:
Hi freesurfer family,
I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain
However, after it finished running it said it was saving "brain", but "brain" was an unknown file type. Am i supposed to specify that somewhere?
Thanks in advance, m
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------- Forwarded message ---------- From: Alistair Perry alistairperry123@gmail.com To: freesurfer@nmr.mgh.harvard.edu Cc: Date: Wed, 5 Sep 2012 13:34:36 +1000 Subject: [Freesurfer] Cortical parcellations and probtrackx2 in diffusion space Hello freesurfer experts,
I know this has been posted elsewhere with the original probtrackx.
I am basically trying to create a surface file from the aseg+aparc.mgz cortical parcellation created when running recon-all. I wish to use this surface file as the seed reference file when performing probtrackx2.
I have succeeded sucessfully in transforming the cortical parcellation into diffusion space, and have created a label file for it.
However, I am having difficulty understanding converting the label file into ascii format, as required for probtrackx2. I am aware that you can convert a label file into ascii format using mri_convert, but you have to specify the lh.white surface file created when performing recon-all. This does not make sense to me for one this label file is not in diffusion space. Plus, why would I only specify one surface hemisphere when I have a label file that lists vertices across both hemispheres?
In the end I am asking whether it is possible/and the best method in creating an ascii surface file of the whole cortical parcellation in diffusion space?
Regards,
Alistair
---------- Forwarded message ---------- From: Jeff Sadino jsadino.queens@gmail.com To: freesurfer@nmr.mgh.harvard.edu Cc: Xin Zhang zhangx@hawaii.edu, Shannon Kogachi skogachi@gmail.com, Eric Cunningham erictcunningham@gmail.com Date: Tue, 4 Sep 2012 18:43:46 -1000 Subject: [Freesurfer] Covary for categorical variable in QDEC Hello,
Is it possible to covary for a categorical variable in QDEC? I see other posters have said it is not possible, but I did not see any official documentation or response regarding the issue.
Thank You, Jeff Sadino
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Katie Bettencourt kcb@wjh.harvard.edu Cc: freesurfer maillist freesurfer@nmr.mgh.harvard.edu Date: Wed, 5 Sep 2012 09:19:06 -0400 (EDT) Subject: Re: [Freesurfer] Repost: Converting BV ROIs to FS Hi Katie
you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try:
select_talairach_point <xtal> <ytal> <ztal>
cheers Bruce
On Tue, 4 Sep 2012, Katie Bettencourt wrote:
Hrm. Ok, is there any way to view data for a subject in Freesurfer on a
talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot?
Katie
On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Katie
I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. KatieThe 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/**compliancelinehttp://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.
---------- Forwarded message ---------- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Cc: Date: Wed, 05 Sep 2012 09:38:36 -0400 Subject: Re: [Freesurfer] repeated measures ANOVA with two groups Hi Shannon, sorry for the delay. There are several ways you can do this. If you already have a slope for each subject, then just use that as input and use the simple two group FSGD file. If you really want to do the RM ANOVA, then there are two ways. The simpler way is to create a "stack" of all subjects for each visit (eg, v1, v2, and v3) using mris_preproc. Next compute paired differences d12 = v1-v2 and d13 = v1-v3 using fscalc (note that you do not need v2-v3). Next, create a new stack from d12 and d13 with mri_concat (eg, mri_concat d12.mgh d13.mgh --o d12+d13.mgh). Then create an FSGD file with a class for each group and two variables (d12 and d13)). The structure will look something like this:
Input subject1 G1 1 0 Input subject2 G1 1 0 ... rest of subjects for group 1 ... Input subject1 G1 0 1 Input subject2 G1 0 1 ... rest of subjects for group 1 ... Input subject1 G2 1 0 Input subject2 G2 1 0 ... rest of subjects for group 2 ... Input subject1 G2 0 1 Input subject2 G2 0 1 ... rest of subjects for group 2 ...
Run the analysis with DOSS. You can use the following contrast matrix to test for an interaction: [1 -1 -1 1]
Let me know if that makes sense or not doug
On 08/23/2012 09:39 PM, Shannon Kogachi wrote:
Hi, Is there a way to set up a repeated measures ANOVA and ANCOVA with two different groups (ex: study group v. controls) and each subject has more than two timepoints? Would it be possible to assign each Input in the fsgd file to two classes (ex: timepoint scan and group) or is there another way to set up the fsgd file and contrast matrices? I've already used qdec in freesurfer 5.1 to calculate rates of change and symmetrized percent changes between the timepoints (using long_mris_slopes) but now would like to perform a repeated measures test. Thank you!
-Shannon K.
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
---------- Forwarded message ---------- From: Help Desk -- Paul Raines help@nmr.mgh.harvard.edu To: Dix Meiberth dix.meiberth@ukb.uni-bonn.de Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Date: Wed, 5 Sep 2012 09:51:17 -0400 (EDT) Subject: Re: [Freesurfer] freesurfer tutorial data Instead of FTP, you could try getting the files via HTTP at
http://surfer.nmr.mgh.harvard.**edu/ftp/dist/freesurfer/http://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/
-- Paul Raines (http://help.nmr.mgh.harvard.**eduhttp://help.nmr.mgh.harvard.edu )
On Tue, 4 Sep 2012 6:19pm, Dix Meiberth wrote:
Thx for your responses. But no, I try to copy to my harddrive on my 1
year old Mac. I think for the fith time right now. There should be no limit but I will doublecheck.
Best regards.
Dix
Von meinem iPhone gesendet
Am 04.09.2012 um 20:56 schrieb Help Desk -- Paul Raines < help@nmr.mgh.harvard.edu>:
2GB sounds like you reaching maybe a file size limit of your operating
system if it is really old. Or if you have are trying to download to a FAT formated external USB drive or such.
-- Paul Raines (http://help.nmr.mgh.harvard.**eduhttp://help.nmr.mgh.harvard.edu )
On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote:
Hi Dix,
not sure what's going on. Have you tried multiple times?
Bruce
On Mon, 3 Sep 2012, Dix.Meiberth@ukb.uni-bonn.de wrote:
Dear sirs and madames,
unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the "bruckner_data_tutorial_subjs.**tar.gz" I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 Dix.Meiberth@ukb.uni-bonn.de
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/**compliancelinehttp://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.
---------- Forwarded message ---------- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Longchuan Li leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Date: Wed, 05 Sep 2012 09:58:20 -0400 Subject: Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri Hi Longchuan, when I asked for the terminal output, I meant the stuff that gets printed to the screen when the command runs. Try running it outside of your script to capture the output. Also, does the old program require 20G ? doug
On 08/27/2012 04:20 PM, Longchuan Li wrote:
Hi, Doug Here is the output from my log file and my command. I have been running this command many times and sometimes the job got killed, but sometimes they finished without error.
/usr/local/sge/bitc/spool/**node13/job_scripts/77912: line 7: 30345 Killed /home/lli/freesurferv51/bin/**mri_label2vol.linux --offset 1 --annot /home/lli/freesurferv51/** subjects/RVJ8_Preuss_20111115/**label/rh.randomroi300_** WithoutMedialWall.**MacaqueYerkes6_to_RVJ8_Preuss_**20111115.annot --temp /home/lli/freesurferv51/**subjects/RVJ8_Preuss_20111115/**mri/brain.mgz --subject RVJ8_Preuss_20111115 --hemi rh --fillthresh 0 --proj frac 0 0.5 0.05 --o /home/lli/freesurferv51/**subjects/RVJ8_Preuss_20111115/** mri/rh.randomroi300_**WithoutMedialWall_Ribbon.** MacaqueYerkes6_to_RVJ8_Preuss_**20111115_fill0_projs0_proje0.**5_projin0.05.nii.gz --identity
Many thanks in advance!
Longchuan
------------------------------**------------------------------**
*From:* Douglas Greve greve@nmr.mgh.harvard.edu *To:* Longchuan Li leonado78@yahoo.com *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu
*Sent:* Monday, August 27, 2012 3:47 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
What is your command line and what is the terminal output? doug
On 8/27/12 7:57 PM, Longchuan Li wrote:
Hi, Doug
This is a follow-up question regarding an updated code you sent to me earlier (mri_label2vol.linux). I noticed that this program frequently takes around ~20G RAM to run and easily get killed by Linux (I supposed) when I ran multiple subjects, because of the large amount of RAM used. Has anyone else proposed the issue? and if so, do you have any suggestions on solving the issue?
Thank you!
Longchuan
------------------------------**------------------------------**
*From:* Leon leonado78@yahoo.com mailto:leonado78@yahoo.com *To:* Douglas N Greve greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu
*Sent:* Friday, June 8, 2012 3:48 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Doug I have run and checked the data and the problem has been perfectly solved. Thank you for the help!
Leon
------------------------------**------------------------------**
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> *To:* Leon leonado78@yahoo.com mailto:leonado78@yahoo.com *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu
*Sent:* Friday, June 8, 2012 1:32 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
I've put a new version of mri_label2vol at that ftp site. When you run it, add "--offset 1". This will change the segmentations IDs to go from 1-162 instead of 0-161. doug
On 06/08/2012 11:30 AM, Leon wrote:
Hi, Douglas
I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161.
Thanks
Leon
PS: I am sending the message again because I was told that the image for the previous mail is too big.
*From:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com> *To:* Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>
*Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi, Douglas
Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1?
I would appreciate your help on this.
Leon
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com> *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>
*Sent:* Thursday, June 7, 2012 2:03 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Leon, I found the problem. mris_make_face_parcellation was actually merging several units together. You can get a fixed version from here: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/mris_make_face_**parcellation.linuxftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
Let me know how it goes doug
On 06/04/2012 02:44 PM, Leon wrote:
Hi, Douglas I have uploaded the file to the system. Also, my new results showed that when ic3.tri (instead of ic2.tri) is used as the input, one ROI at the similar location is also
missing.
Hope it will help you diagnose.
Thanks Leon
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu<mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>>
*To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>>
*Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>>
*Sent:* Monday, June 4, 2012 1:00 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
Can you upload the subject to our file drop system?
www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<
http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
On 06/04/2012 12:24 PM, Leon wrote:
Hi, Douglas
Thank you very much for the updated one. I tested the new codes and the problem is still there. The ID for the original version that generates a mask with one missing ROI is:
$Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
I remember this is a version I downloaded from a link in FS
archive.
The ID for the one you sent to me is:
$Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
They look almost identical. Do you have any ideas what else may
cause
this issue and possible workaround?
Thank you
Leon
*From:* Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu<mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu<mailto:
greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>>>
*To:* freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.**
harvard.edu freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>>
*Sent:* Friday, June 1, 2012 11:29 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri
What version are you using? I fix a problem last Sept that might be like this. I've put a new version of mri_label2vol here:
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
greve/mri_label2vol.linuxftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
Try this and let me know if it works. doug
On 6/1/12 10:46 PM, Leon wrote: > Hi, Bruce > Here are my two command lines > For transferring the annot from the source template to the target > subject: > > /home/freesurfer/bin/mri_**surf2surf --srcsubject ${srcsubject} > --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval > src_2_trg.annot --hemi rh --surfreg sphere.reg0 > > Where sphere.reg0 is the registration from the target subject to
the
> source subject. > > For transfer them to the volume file: > > /home/freesurfer/bin/mri_**label2vol --annot src_2_trg.annot
--temp
> ${fs_dir}/${trgsubject}/mri/**brain.mgz --subject ${trgsubject}
--hemi
> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz > --identity > > > Here is output for one of my transformations: > > Setting mapmethod to nnf > Source registration surface changed to sphere.reg0 > Target registration surface changed to sphere.reg0 > srcsubject = MacaqueA > srcval = (null) > srctype = > trgsubject = MacaqueB > trgval = >
/home/freesurfer/freesurfer/**subjects/MacaqueB/label/rh.**
MacaqueA_to_MacaqueB.annot
> trgtype = > srcsurfreg = sphere.reg0 > trgsurfreg = sphere.reg0 > srchemi = rh > trghemi = rh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > label-src = (null) > label-trg = (null) > OKToRevFaceOrder = 1 > Reading source surface reg > /home/freesurfer/freesurfer/**subjects/MacaqueA/surf/rh.**
sphere.reg0
> Loading source data > Reading surface file > /home/freesurfer/freesurfer/**subjects/MacaqueA/surf/rh.orig > reading colortable from annotation file... > colortable with 162 entries read (originally > /usr/local/freesurfer/lib/bem/**ic2.tri) > Reading target surface reg > /home/freesurfer/freesurfer/**subjects/MacaqueB/surf/rh.**
sphere.reg0
> Done > Mapping Source Volume onto Source Subject Surface > surf2surf_nnfr: building source hash (res=16). > Surf2Surf: Forward Loop (61916) > > Surf2Surf: Dividing by number of hits (61916) > INFO: nSrcLost = 17467 > nTrg121 = 61916, nTrgMulti = 0, MnTrgMultiHits = 0 > nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910,
MnSrcMultiHits
> = 0.920927 > Saving target data > Converting to target annot > Saving to target annot >
/home/freesurfer/freesurfer/**subjects/MacaqueB/label/rh.**
MacaqueA_to_MacaqueB.annot
> step2: writing the surface label to volume... > Number of labels: 0 > Annot File: >
/home/freesurfer/freesurfer/**subjects/MacaqueB/label/rh.**
MacaqueA_to_MacaqueB.annot
> Template Volume: > /home/freesurfer/freesurfer/**subjects/MacaqueB/mri/brain.**mgz > Outut Volume: >
/home/freesurfer/freesurfer/**subjects/MacaqueB/mri/rh_**
MacaqueA_to_MacaqueB_fill0_**porjs0.3_proje0.8_projin0.05.**mgz
> Registration File: (null) > Fill Threshold: 0 > Label Vox Vol: 1 > ProjType: frac > ProjTypeId: 2 > ProjStart: 0.3 > ProjStop: 0.8 > ProjDelta: 0.05 > Subject: MacaqueB > Hemi: rh > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $ > Template RAS-to-Vox: -------- > -1.000 -0.000 -0.000 160.000; > -0.000 -0.000 -1.000 160.000; > -0.000 1.000 -0.000 160.000; > -0.000 -0.000 -0.000 1.000; > Template Voxel Volume: 1 > nHits Thresh: 0 > Using Identity Matrix > RegMat: -------- > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -1.000 0.000 0.000 160.000; > 0.000 0.000 -1.000 160.000; > 0.000 1.000 0.000 160.000; > 0.000 0.000 0.000 1.000; > INFO: loading surface > /home/freesurfer/freesurfer/**subjects/MacaqueB/surf/rh.**white > nvertices = 61916 > Reading thickness > /home/freesurfer/freesurfer/**subjects/MacaqueB/surf/rh.**
thickness
> Loading annotations from >
/home/freesurfer/freesurfer/**subjects/MacaqueB/label/rh.**
MacaqueA_to_MacaqueB.annot
> reading colortable from annotation file... > colortable with 162 entries read (originally > /usr/local/freesurfer/lib/bem/**ic2.tri) > annotidmax = 162 > Allocating Hit Volume (1013448704) voxels > nlabels = 162 > > PVF (null) > Thesholding hit volume. > mri_label2vol done > > *From:* Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:
fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu<mailto:
fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu>>
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> <mailto:fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu<mailto:
fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu>
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<mailto:fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu<mailto:
fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu>>>>
> *To:* Leon <leonado78@yahoo.com mailto:leonado78@yahoo.com
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com <mailto:
leonado78@yahoo.com mailto:leonado78@yahoo.com>>**>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com <mailto:
leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com <mailto:
leonado78@yahoo.com mailto:leonado78@yahoo.com>>**>
> *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>>>
> <mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.**harvard.edufreesurfer@nmr.mgh.harvard.edu<mailto:
freesurfer@nmr.mgh.**harvard.edu freesurfer@nmr.mgh.harvard.edu>>>>
> *Sent:* Friday, June 1, 2012 8:02 PM > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol
to
> transfer ic2.tri > > Can you send us your command lines and screen output? > > > > On Jun 1, 2012, at 7:44 PM, Leon <leonado78@yahoo.com <mailto:
leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com <mailto:
leonado78@yahoo.com mailto:leonado78@yahoo.com>>
> <mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com <mailto:
leonado78@yahoo.com mailto:leonado78@yahoo.com>
<mailto:leonado78@yahoo.com mailto:leonado78@yahoo.com <mailto:
leonado78@yahoo.com mailto:leonado78@yahoo.com>>**>> wrote:
> >> Hi, folks >> >> when I transferred the annotation file obtained using >> mri_make_face_parcellation based on ic2 (162 labels) to a volume >> file using mri_label2vol, I found that one ROI patch was missing
in
>> the volume file (see attached). I searched archives and the
closest
>> thread I could found is that somebody reported an ROI with the
last
>> index was missing in the mgz file after they were transferred
from
>> the annotation file to the volume file. >> >> Could someone help on this? If this happens to be a bug, is there >> any other strategy that will allow me to get a GM/WM ribbon
without
>> a hole on it? >> >> Many thanks in advance >> Leon >> <MissingROI.jpg> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**
harvard.edu Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu<mailto:
Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>>
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>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**
harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>>>>
> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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 <mailto:Freesurfer@nmr.mgh.**
harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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---------- Forwarded message ---------- From: Varghese Chikku chikkuv@tcd.ie To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Date: Wed, 5 Sep 2012 16:01:08 +0200 Subject: Re: [Freesurfer] Freesurfer-Error message
Thanks Bruce,
Still no luck,this what I am getting
/freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid test7 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects
Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
/home/virtualuser/freesurfer/subjects/test7
mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz
mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz
file not found or unknown file type for file /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012
For more details, see the log file /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FreeSurfer:~/freesurfer/subjects/test1>
On 4 September 2012 14:37, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
if that's the name of the image file. Can you post the list on your replies so others can answer?
thanks Bruce
On Tue, 4 Sep 2012, Varghese Chikku wrote:
Hi Bruce,
Many thanks for you mail. Is this the command you referring to. recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.* *dcm -subjid test4 Thanks Chikku
On 3 September 2012 17:33, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Chikku
you need to give it the path to an image file (any one will do)and it will figure out the other slices that makeup the same series. What is the resolution of your data? 50 slices isn't usually enough to cover the brain at high enough resolution to get good thickness results.
cheers Bruce On Mon, 3 Sep 2012, Varghese Chikku wrote: Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre-subjid test2
I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/**raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp$ reading from /media/sf_freesurferstudys/** raw/raw_scr/T1pre... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012
My image files, in dcm format, are at /media/sf_freesurferstudys/**raw/raw_scr/T1pre : /media/sf_freesurferstudys/**raw/raw_scr/T1pre> ls Image00001 Image00010 Image00019 Image00028 Image00037Image00046 Image00002 Image00011 Image00020 Image00029 Image00038 Image00047 Image00003 Image00012 Image00021 Image00030 Image00039 Image00048 Image00004 Image00013 Image00022 Image00031 Image00040 Image00049 Image00005 Image00014 Image00023 Image00032 Image00041 Image00050 Image00006 Image00015 Image00024 Image00033 Image00042 Image00007 Image00016 Image00025 Image00034 Image00043 Image00008 Image00017 Image00026 Image00035 Image00044 Image00009 Image00018 Image00027 Image00036 Image00045
Many thanks for your help. chikkuThe 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/**compliancelinehttp://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.
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: "Varghese, Chikku" Chikku.Varghese@perceptive.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Date: Wed, 5 Sep 2012 10:07:22 -0400 (EDT) Subject: Re: [Freesurfer] Freesurfer-Error message Is that the actual name of the file? Does it have a dcm extension? On Wed, 5 Sep 2012, Varghese, Chikku wrote:
Thanks Bruce,
Still no luck,this what I am getting
/freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/** raw/raw_scr/T1pre/Image00001.**dcm -subjid test7 -all Subject Stamp: freesurfer-Linux-centos4-**stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-**stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/**subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/**subjects/test7
mri_convert /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.**dcm /home/virtualuser/freesurfer/**subjects/test7/mri/orig/001.**mgz
mri_convert /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.**dcm /home/virtualuser/freesurfer/**subjects/test7/mri/orig/001.**mgz file not found or unknown file type for file /media/sf_freesurferstudys/* *raw/raw_scr/T1pre/Image00001.**dcm Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012
For more details, see the log file /home/virtualuser/freesurfer/** subjects/test7/scripts/recon-**all.log To report a problem, see http://surfer.nmr.mgh.harvard.** edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FreeSurfer:~/freesurfer/**subjects/test1>
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.**harvard.edufischl@nmr.mgh.harvard.edu ] Sent: Dienstag, 4. September 2012 18:25 To: Varghese, Chikku Subject: Re: [Freesurfer] Freesurfer-Error message
you need a -all at the end to tell it what to do. And please cc the list so others can answer!
On Tue, 4 Sep 2012, Varghese, Chikku wrote:
recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.**dcm -subjid test4
Is it this command I should use?
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---------- Forwarded message ---------- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Cc: Date: Wed, 05 Sep 2012 10:47:59 -0400 Subject: Re: [Freesurfer] FDR Correction of NHP Surface Data Hi Clark, I just made a modification to mri_binarize to make it take an FDR as input. It computes the threshold and binarizes the input based on the threshold. I've put a copy here:
ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/mri_binarize.linuxftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize.linux
Run it with --help to get more info.
doug
On 08/29/2012 02:08 PM, Clark Fisher wrote:
Hi Sebastian,
I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model.
At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well.
I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own.
-Clark
On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote:
Hi Clark,
On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer).
Does it really correct the map? I thought all it does is figureout the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps… (then again, I do not know any statistician...)
best Sebastian
I recognize that this may not be an officially supported functionality,
but is there some way to save the adjusted overlays from tksurfer, or create them in some other way?
Best, Clark
On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote:
Hi Clark
you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface.
cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short
version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moeller@caltech.edu
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