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30132 discussions

total wm volume calculation
by Zhang, Yuning 23 Sep '11

23 Sep '11

Dear FreeSurfer Expert, i am trying to generate the total wm volume using mris_wm_volume <subjid> <hemi> ,but this value is different from what i get using mirs_volume ?h.white, could you explain the differences between these two commands. and which is the best representation of the surface based total wm volume ? thanks yuning

2 1

QDEC and Cortical Thickenss
by Antonella Kis 23 Sep '11

23 Sep '11

Hi Doug, Many thanks for the valuable answer and help. I would appreciate a lot if you can advise me how I can get in a table from QDEC the clusters after I find the clusters and also the mean value for the cortical thickness within this clusters. I know in GLM the files are coming as an output but I cannot see in QDEC this files. The same question for the values after running FDR in QDEC. My last question is what should I do if for one case I get error when I do FDR and thresh is becoming 3.18 (instead of 2) and QDEC cannot run the statistics for the clusters. Also it is possible to get more clusters after running FDR in comparison with the no. of clusters when I set up the thresh 2? Thank you very much and have a great weekend! Antonella ________________________________ From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com>; freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Thursday, September 22, 2011 3:53 PM Subject: Re: [Freesurfer] Contrast Vector while eliminating age and gender If you want to "eliminate" age and gender, you have to include them in the model. In this case, they are called "nuisance" regressors. But this is just an arbitrary name. The model is constructed of regressors, some of which you care about and some you don't, but the GLM is run in the same way regardless. Where the difference comes is when you go to construct contrast vectors. If you want to treat some regressors as nuisance, then put a 0 in their column in the contrast vector. doug Antonella Kis wrote: > Hi Doug, > > Yes, I looked online but in all the examples I found age was included > in the study. The same thing for qdec all the examples I saw online > are related to a study (a comparison between two groups) but > considering age. > > I couldn't find any documentation for a study between two groups while > eliminating age and gender. > > Please advise and sorry for all this questions. > Regards, > Antonella > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, September 22, 2011 12:03 PM > *Subject:* Re: [Freesurfer] Contrast Vector while eliminating age and > gender > > Have you looked at the FSGD examples on the wiki? Do a search for FSGD. > doug > > Antonella Kis wrote: > > > > > > > > Dear All, > > > > What should be my contrast vector if I want to do a direct comparison > > between groups (patients vs. controls) after eliminating gender and > > age? Should this be [1 -1]? > > > > Should I change my FSGD in order to be able to compare between > > patients and controls accounting for age (I want to make sure that the > > age does not confound my results). Please see attached my FSGD file. > > > > Also, my question is how the clusters are created: the clusters > > formation is due to a similar value within cortical > > thickness(cortical thickness with similar values from patients and > > controls are grouped together in a cluster (e.g. cluster no.1) while > > other cortical thickness values are forming different clusters) or the > > clusters are formed based on age -age grouping (each subject belong to > > an age cluster)? > > > > Thank you, > > AK > > > > > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

tracula - if expression syntax
by Judit Haasz 23 Sep '11

23 Sep '11

Hi, I have been running tracula on a Linux machine, without a problem. Now I am trying to run tracula on a Mac-Pro machine (running Mac OS X version 10.7.1 - Lion). I followed the tutorial and set up the requested structure and configuration file. When I try running the preprocessing step (trac-all -prep -c ./scripts/dmrirc, both in bash and tcsh) I get the following message: If: expression syntax. Do u have some suggestions that i could try to overcome the problem? thanks, Judit

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Re: [Freesurfer] Recon-all Error: _FindFacePath
by Louis Nicholas Vinke 23 Sep '11

23 Sep '11

Hi Daniel, Both of the cases you sent us had a fair amount of neck/spine remaining after the skullstrip step which caused mris_fix_topology to fail. I processed both cases again using the following command and recon-all finished without errors: recon-all -skullstrip -autorecon2 -autorecon3 -s [SubjID] Sometimes running the skullstrip step a second time can get rid of or reduce large portions of skull/dura which were not removed during the first pass. With those two cases there is still some skull/dura left which you could try to remove by playing with the skullstrip watershed parameters. See this wiki page for details: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix -Louis >> From: "Daniel Ferreira Padilla" <danifer(a)ull.es> >> Date: September 15, 2011 5:48:30 AM EDT >> To: <fischl(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Recon-all Error: _FindFacePath >> > >> Dear Bruce, >> >> >> >> Thank you very much. I have uploaded these two subjects to the file drop linked to your email (fischl(a)nmr.mgh.harvard.edu) It should be going to you. >> >> >> >> Thanks again >> >> >> >> Daniel Ferreira >

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Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
by Lauge Emil Borch Laurs S0rensen 23 Sep '11

23 Sep '11

Hi Martin, Thanks for the cope-snippet. A small C program based on that revealed that it is a problem with popen (gzip is installed and working properly, and exchanging gzip with other programs produced the same error). Error code 38 (ENOSYS) means "Function not implemented". So the problem appears to be popen not working properly on our system. We will now update the system. Thanks for the info! Cheers Lauge On Thu, Sep 22, 2011 at 19:07, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > Hi Lauge, > > is gzip installed/working? > > this is the code around that block (so you are right, it happens when > popen tries to call gzip). I could not find out what error 38 means. > > Best, Martin > > char command[STRLEN]; > // write gzipped file > myclose=pclose; > strcpy(command, "gzip -f -c > " ); > if (strlen(command) + strlen(fname) >= STRLEN-1) > ErrorReturn > (ERROR_BADPARM, > (ERROR_BADPARM, > "%s:GCAMwrite(%s): gzip command line too long (%d)", \ > Progname,fname, STRLEN)); > strcat(command, fname); > errno=0; > printf("GCAMwrite:: the command is: %s\n",command); > fp = popen(command, "w"); > if (errno) > { > printf("GCAMwrite:: the popen error code is: %d\n",errno); > if (fp) > pclose(fp); > errno = 0; > ErrorReturn > (ERROR_BADPARM, > (ERROR_BADPARM, > "GCAMwrite(%s): gzip encountered error.", > fname)) ; > }

1 0

Re: [Freesurfer] Contrast Vector while eliminating age and gender
by Douglas N Greve 22 Sep '11

22 Sep '11

If you want to "eliminate" age and gender, you have to include them in the model. In this case, they are called "nuisance" regressors. But this is just an arbitrary name. The model is constructed of regressors, some of which you care about and some you don't, but the GLM is run in the same way regardless. Where the difference comes is when you go to construct contrast vectors. If you want to treat some regressors as nuisance, then put a 0 in their column in the contrast vector. doug Antonella Kis wrote: > Hi Doug, > > Yes, I looked online but in all the examples I found age was included > in the study. The same thing for qdec all the examples I saw online > are related to a study (a comparison between two groups) but > considering age. > > I couldn't find any documentation for a study between two groups while > eliminating age and gender. > > Please advise and sorry for all this questions. > Regards, > Antonella > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, September 22, 2011 12:03 PM > *Subject:* Re: [Freesurfer] Contrast Vector while eliminating age and > gender > > Have you looked at the FSGD examples on the wiki? Do a search for FSGD. > doug > > Antonella Kis wrote: > > > > > > > > Dear All, > > > > What should be my contrast vector if I want to do a direct comparison > > between groups (patients vs. controls) after eliminating gender and > > age? Should this be [1 -1]? > > > > Should I change my FSGD in order to be able to compare between > > patients and controls accounting for age (I want to make sure that the > > age does not confound my results). Please see attached my FSGD file. > > > > Also, my question is how the clusters are created: the clusters > > formation is due to a similar value within cortical > > thickness(cortical thickness with similar values from patients and > > controls are grouped together in a cluster (e.g. cluster no.1) while > > other cortical thickness values are forming different clusters) or the > > clusters are formed based on age -age grouping (each subject belong to > > an age cluster)? > > > > Thank you, > > AK > > > > > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

1 0

tksurfer display
by Peter Glynn 22 Sep '11

22 Sep '11

Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn

3 7

mri_watershed for inner_skull_surface question
by Roderick McColl 22 Sep '11

22 Sep '11

Hi all, Trying to get mri_watershed to give me a good inner_skull_surface, which I want to combine with the pial surface to estimate sulcal CSF, as I don't see any other way. Unfortunately the data I have tested on all generate unreliable inner_skull surfaces. Can anyone provide a tip for optimizing the result? Thanks -roddy ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 2

Discrete and Continuous factors in QDEC
by Antonella Kis 22 Sep '11

22 Sep '11

Hi Doug, One more question please: if I want to do a cortical thickness study between two groups (patients and controls) and I want to eliminate the age and gender what should be my Discrete and Continuous factors in QDEC? Thank you. AK

2 1

Problem writing talairach.m3z in mri_ca_register
by Lauge Emil Borch Laurs S0rensen 22 Sep '11

22 Sep '11

Hi, I am running FreeSurfer on ADNI data and get an error when mri_ca_register attempts to write to transforms/talairach.m3z using gzip. I run the full FreeSurfer pipeline using a bash script containing the following: #!/bin/bash export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/lauges/storage /usr/local/freesurfer/bin/recon-all -i /image/data2/ADNI/009_S_0751/MP_RAGE/2006-07-25_12_31_19.0/S17487/ ADNI_009_S_0751_MR_MP_RAGE__br_raw_20060801143246276_1_S17487_I20013.dcm -s 009_S_0751 -all The error appears to happen when mri_ca_register writes using gzip through a pipe and the popen error code is 38. This is not a memory nor a space issue since there is plenty of both available. As far as I now, error code 38 may be related to too many pipes being open at once, but I am not sure of this. Excerpt from 009_S_0751/scripts/recon-all.log: ... GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is: 38 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Thu Sep 15 23:43:42 CEST 2011 /storage/lauges/009_S_0751/mri mri_ca_register -invert-and-save transforms/talairach.m3z GCAMread: encountered error executing: 'zcat transforms/talairach.m3z' Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux imageserver1 2.6.20-gentoo-r8 #2 SMP Fri May 25 10:23:59 CEST 2007 x86_64 Intel(R) Xeon(R) CPU X5355 @ 2.66GHz GenuineIntel GNU/Linux Best, Lauge

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