Re: [Freesurfer] Difference in GMV generated from qdec and mris_anatomical_stats
Dear All, Sorry for this email. I think I made some mistakes. When I redone the analysis, the values were same. Kindly ignore the email. From: Anupa AV av.an...@yahoo.com To: Freesurfer freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Thursday, October 3, 2013 11:06 AM Subject: Difference in GMV generated from qdec and mris_anatomical_stats Dear FS experts, I was trying to find the gray matter volume of superior temporal gyrus (STG) for schizophrenia patients using freesurfer. I ran recon-all and generated the rh/lh.aparc.volume.stats using qdec. From that, I got the volume for left hand lh_superiortemporal_volume,=11893. Out of curiosity, I separately found the STG volume for this patient alone using the follo. steps. 1. Saved the label lh.STG using tksurfer -annot aparc SZ01 lh pial 2. Then generated the volume using mris_anatomical_stats. 3. I found the value to be 16268. I'm wondering why there is so much changes in the generation of GM volumes. Can anyone please help me with my query?___ 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] Difference in GMV generated from qdec and mris_anatomical_stats
Dear FS experts, I was trying to find the gray matter volume of superior temporal gyrus (STG) for schizophrenia patients using freesurfer. I ran recon-all and generated the rh/lh.aparc.volume.stats using qdec. From that, I got the volume for left hand lh_superiortemporal_volume,=11893. Out of curiosity, I separately found the STG volume for this patient alone using the follo. steps. 1. Saved the label lh.STG using tksurfer -annot aparc SZ01 lh pial 2. Then generated the volume using mris_anatomical_stats. 3. I found the value to be 16268. I'm wondering why there is so much changes in the generation of GM volumes. Can anyone please help me with my query? ___ 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] recon-all-hippo-subfeilds
Dear FS experts, I've a query regarding the recon-all analysis. I ran recon-all using the following command eg. recon-all -i location/nc.nii -s NC -all I got the analysis done. Now I'm interested to calculate the hippocampal structures. I knw the command line for that also recon-all -i location/nc.nii -s NC -all -hippo-subfields Problem for me is that I've 45 subjects. I ran recon-all without hippo-subfields commands. i.e. from motion correction to Ex-vivo Entorhinal Cortex Label rh. (log file) Is there any way to do hippo-sufields alone than running the whole steps again (which is very time consuming). Thanks in advance. ___ 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] recon-all-hippo-subfeilds
Dear Koen, It worked... Thanks a lot From: Koen Van Leemput k...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Freesurfer Mailinglist freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Thursday, September 19, 2013 12:48 PM Subject: Re: [Freesurfer] recon-all-hippo-subfeilds Hi, I believe recon-all -s NC -hippo-subfields should do that. Please let us know if it doesn't. Koen On Sep 19, 2013 9:00 AM, Anupa AV av.an...@yahoo.com wrote: Dear FS experts, I've a query regarding the recon-all analysis. I ran recon-all using the following command eg. recon-all -i location/nc.nii -s NC -all I got the analysis done. Now I'm interested to calculate the hippocampal structures. I knw the command line for that also recon-all -i location/nc.nii -s NC -all -hippo-subfields Problem for me is that I've 45 subjects. I ran recon-all without hippo-subfields commands. i.e. from motion correction to Ex-vivo Entorhinal Cortex Label rh. (log file) Is there any way to do hippo-sufields alone than running the whole steps again (which is very time consuming). Thanks in advance. ___ 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] recon-all for multiple subjects
Dear All, This worked for me... for x in SZ1 SZ2 SZ3 do recon-all -i $x.nii -s $x -all -hippo-subfileds done Thanks for your valuable inputs... From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Watson, Christopher christopher.wat...@childrens.harvard.edu Cc: Anupa AV av.an...@yahoo.com; KOOL p.c.m.p.koolsch...@uva.nl; Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, September 7, 2013 7:10 PM Subject: Re: [Freesurfer] recon-all for multiple subjects it won't handle it. If you gave it multiple inputs each with it's own -i it would assume that they are different images of the same subject and perform motion correction and averaging. I don't think that is the case here - you want to give each instance of recon-all a single nifti volume as input (unless you acquired multiple T1-weighted images/session) cheers Bruce On Sat, 7 Sep 2013, Watson, Christopher wrote: The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anupa AV [av.an...@yahoo.com] Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working ___ 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.
[Freesurfer] version 2 FS
Dear SIr, I made some analysis based on FS v.2.0. Does the Deprecated version means that the results generated by FSv.2 can't be published??? ___ 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] recon-all for multiple subjects
Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working ___ 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] version 2 FS
I really meant FS5.2.. Sorry for the lack of clarity of my prev. mail From: Anupa AV av.an...@yahoo.com To: Freesurfer freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Saturday, September 7, 2013 3:14 PM Subject: version 2 FS Dear SIr, I made some analysis based on FS v.2.0. Does the Deprecated version means that the results generated by FSv.2 can't be published???___ 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] recon-all -aseg.stats doubt
Dear FS experts, I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 for my analysis. After recon-all with hippo-subfield, only 45 brain volumes were genreated in aseg.stats file. Freesurfer v.5.1 analysis were able to generate cortical structure's volumes also. Where v.5.2 mainly generated subcortical volumes like caudate. putamen, amygdala and so on. MAy I knw, is there any way to generate cortical structures also using recon-all command.. Any help 'll be greatly appreciated.___ 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] recon-all -aseg.stats doubt
Dear FS experts, I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 for my analysis. After recon-all with hippo-subfield, only 45 brain volumes were genreated in aseg.stats file. Freesurfer v.5.1 analysis were able to generate cortical structure's volumes also. Where v.5.2 mainly generated subcortical volumes like caudate. putamen, amygdala and so on. MAy I knw, is there any way to generate cortical structures also using recon-all command.. Any help 'll be greatly appreciated.___ 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] Qdec error
Dear All, When I tried to running qdec, I'm getting the following error. qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory What is the solution for this.? Any help will be greatly appreciated. ___ 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] Doubts on bblabel
Dear FS experts, By definition bblabel means.. Applies a bounding box to a label. The bounding box is specified by six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label points within this box are copied to the output. If a min is not specified, then -infinity is used. If a max is not specified, then +infinity is used. Example: bblabel --l lh.G_cuneus.label --o lh.out.label \ --xmin 0 --ymax -90 --zmin 10 --zmax 20 Keeps label points from lh.G_cuneus.label that have x 0, y -90, and z between 10 and 20. The result is stored in lh.out.label. IN THE ABOVE MENTIONED EXAMPLE, WHAT IS THE BASIS FOR THE SELECTION OF X, Y, Z VALUES??___ 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] Dimension of brain
Dear FS experts, I'd like to know the fsaverage brain (rendered brain) generated after recon-all analysis is same as that of individuals brain size. I mean is rendered brain developed after recon-all = individual brain?? If not, How much cm/mm away or towards the original brain?? ___ 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] Merging labels for multiple data sets
Dear All, I am having a total of 100 subjects for my analysis. My aim is to seperate DLPFC by making coronal cuts. I know the procedure to do for single subjects. Can anyone help me with the command line for mutiple data sets..? Any help will be greatly appreciated.. ___ 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] register.dat
Dear All, I was trying to create register.dat for a single subject. Command line: autoreg-sess -s SZ01 -d $SUBJECTS_DIR/SZ01 But it showed some error like this... Logfile is /home/mbial/JPJ/freesurfer/SZ01/log/autoreg-sess.log setenv SUBJECTS_DIR /home/mbial/JPJ/freesurfer/SZ01 ___ --- ERROR: --- ___ Inside the log I got some thing like this: autreg-sess log file $Id: autoreg-sess,v 1.4 2007/01/09 22:41:16 nicks Exp $ /usr/local/freesurfer/fsfast/bin/autoreg-sess Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux Tue Apr 23 14:11:09 IST 2013 setenv SUBJECTS_DIR /home/mbial/JPJ/freesurfer/SZ01 ___ --- ERROR: --- ___ What might be the trouble with this..? Please 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] Merging the labels to T1 image
Dear Ghosh, I tried to use the overlay command. tkmedit -f /home/mbial/JPJ/freesurfer/SZ01/mri/brain.mgz -overlay DLPFC.label Kindly check whether the command line is correct or not. But it's throwing some error. Error: Loading functional overlay ./DLPFC.label Couldn't load MRI volume. Tkmedit couldn't read the functional volume you specified. This could be because the volume wasn't found or was unreadable, or because a valid header type couldn't be find, or a registration file couldn't be found or opened. From: Shantanu Ghosh shant...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu; Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 9:44 AM Subject: Re: [Freesurfer] Merging the labels to T1 image Hi Anupa- you can use tkmedit with -overlay flag shantanu On Sat, April 20, 2013 10:56 pm, Anupa AV wrote: Ok... I mean overlaying the label to T1W image Fm: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 8:09 AM Subject: Re: [Freesurfer] Merging the labels to T1 image Sorry, I still don't understand. What do you mean by merge? On Apr 20, 2013, at 10:37 PM, Anupa AV av.an...@yahoo.com wrote: Dear Bruce, Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS? From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image Hi Anupa I'm not sure what you mean, but mri_label2vol might do what you want cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote: Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image? If yes, which method I should follow? ___ 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 -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging___ 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] Merging the labels to T1 image
Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image? If yes, which method I should follow? ___ 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] Merging the labels to T1 image
Dear Bruce, Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS? From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image Hi Anupa I'm not sure what you mean, but mri_label2vol might do what you want cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote: Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image? If yes, which method I should follow? ___ 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] Merging the labels to T1 image
Ok... I mean overlaying the label to T1W image Fm: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 8:09 AM Subject: Re: [Freesurfer] Merging the labels to T1 image Sorry, I still don't understand. What do you mean by merge? On Apr 20, 2013, at 10:37 PM, Anupa AV av.an...@yahoo.com wrote: Dear Bruce, Sorry and to be more precise... After creating a label, say DLPFC, I want to merge it on the subject's T1 sagittal section. I'd like to know whether that's possible with FS? From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image Hi Anupa I'm not sure what you mean, but mri_label2vol might do what you want cheers Bruce On Fri, 19 Apr 2013, Anupa AV wrote: Dear FS experts, Is it possible to merge the label obtained from tksurfer to T1 weighted image? If yes, which method I should follow? ___ 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.
[Freesurfer] error while performing recon-all for multiple datasets
Dear All, I want to run recon-all for multiple subjects. I named my sbjects as SZ01.nii, SZ02.nii etc. After setting the cd and environmanet variable, I ran using following for loop: for x in * do recon-all -i SZ*.nii -s $x -all done I got the following error: WHAT MIGHT BE THE REASON FOR THE ERROR??? WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ01.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ02.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ03.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: Flag SZ02.nii unrecognized. -i SZ01.nii SZ02.nii SZ03.nii SZ04.nii -s SZ04.nii -all Linux mbial-HP-Z210-Workstation 3.2.0-40-generic-pae #64-Ubuntu SMP Mon Mar 25 21:44:41 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 19 11:43:24 IST 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting___ 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 to calcutate Brain volume?
Dear All, I went thru the link suggested by Mr. Cedric.https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009600.html From that mail I understood how to create the label for multiple subjects. I already created a DLPFC for one individual. I want to know how to measure the corticla volume (mm3) of that created DLPFC. Any helps'll be greatly appreciated. From: Anupa AV av.an...@yahoo.com To: Koolschijn, Cédric p.c.m.p.koolsch...@uva.nl; Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Monday, April 15, 2013 2:50 PM Subject: Re: [Freesurfer] How to calcutate Brain volume? Dear Cedric, Thanks a bunch. I'll try with mri_label2label. From: Koolschijn, Cédric p.c.m.p.koolsch...@uva.nl To: Anupa AV av.an...@yahoo.com Sent: Monday, April 15, 2013 1:07 PM Subject: Re: [Freesurfer] How to calcutate Brain volume? Dear Anupa, The DLPFC is not a standard label in FS. So you need to create it yourself by merging the following labels: DLPFC: middle frontal gyrus, and inferior and middle frontal sulci See also: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009600.html Best, Cédric P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism ADHD Research Center Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E p.c.m.p.koolsch...@uva.nl W http://www.dutcharc.nl// On 4/15/13 7:34 AM, Anupa AV av.an...@yahoo.com wrote: Dear FreeSurfer Experts, I'd like to know how to measure the volume of a brain region using freesurfer. I know to obtain the volumes after runnin recon-all command. But I don't find the brain volume of my interest which is DLPFC. How can I get the brain volume of my interest.? Thanks for your response in advance. ___ 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 to calcutate Brain volume?
Dear Cedric, Thanks a bunch. I'll try with mri_label2label. From: Koolschijn, Cédric p.c.m.p.koolsch...@uva.nl To: Anupa AV av.an...@yahoo.com Sent: Monday, April 15, 2013 1:07 PM Subject: Re: [Freesurfer] How to calcutate Brain volume? Dear Anupa, The DLPFC is not a standard label in FS. So you need to create it yourself by merging the following labels: DLPFC: middle frontal gyrus, and inferior and middle frontal sulci See also: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009600.html Best, Cédric P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism ADHD Research Center Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E p.c.m.p.koolsch...@uva.nl W http://www.dutcharc.nl// On 4/15/13 7:34 AM, Anupa AV av.an...@yahoo.com wrote: Dear FreeSurfer Experts, I'd like to know how to measure the volume of a brain region using freesurfer. I know to obtain the volumes after runnin recon-all command. But I don't find the brain volume of my interest which is DLPFC. How can I get the brain volume of my interest.? Thanks for your response in advance. ___ 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] 32 bit ubuntu in a 64 bit workstation- Problem
Dear All, I'm working with a system, where 32 bit ubuntu is loaded on to a 64 bit computer. Previously there were graphics problem (Screen gets stuck-- So I restarts it and 'll log in again). Now I'm facing a problem where I cannot enter into ubuntu. Any solutions for this problem will be greatly appreciated.___ 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] recon-all for multiple subjects using for loop
Dear FS experts, I'd like to know about the for loop command for running recon-all for multiple subjects. I went thru this link, https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2006-November/004083.html But didn't get much info. Can anyone please tell me how to run recon-all for multiple subjects? Thanks in advance.___ 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 to calcutate Brain volume?
Dear FreeSurfer Experts, I'd like to know how to measure the volume of a brain region using freesurfer. I know to obtain the volumes after runnin recon-all command. But I don't find the brain volume of my interest which is DLPFC. How can I get the brain volume of my interest.? Thanks for your response in advance.___ 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] bblabel values for DLPFC
Dear Doug, I used bblabel for making coronal cut. The definition is given below. bblabel Applies a bounding box to a label. The bounding box is specified by six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label points within this box are copied to the output. If a min is not specified, then -infinity is used. If a max is not specified, then +infinity is used. Example: bblabel --l lh.G_cuneus.label --o lh.out.label --xmin 0 --ymax -90 --zmin 10 --zmax 20 Keeps label points from lh.G_cuneus.label that have x 0, y -90, and z between 10 and 20. The result is stored in lh.out.label. So I suppose, there would be X, Y, Z values for DLPFC region also.It's ok, if you don't know much about it. Thanks for your support. From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 12:22 AM Subject: Re: [Freesurfer] bblabel values for DLPFC I don't know that there is such a definition of DLPFC. doug On 04/09/2013 04:52 AM, Anupa AV wrote: Dear All, I 'd like to know the xmin, ymin and zmin for creating DLPFC label using bblabel string. I want to make a coronal cut at y=26 for seperating DLPFC from premotor cortex. I tried by giving a value of xmin=0, ymin=26 and zmin= 0. I'd like to know whether I'm on right track. Thanks in advance for your response. ___ 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 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] bblabel values for DLPFC
Dear All, I 'd like to know the xmin, ymin and zmin for creating DLPFC label using bblabel string. I want to make a coronal cut at y=26 for seperating DLPFC from premotor cortex. I tried by giving a value of xmin=0, ymin=26 and zmin= 0. I'd like to know whether I'm on right track. Thanks in advance for your response. ___ 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] bblabels??
Hello experts, I'm in a process to make coronal cuts using tksurfer Please help me with the following questions: 1. How to map the label(merged) to fsaverage? 2. How to use bblabels? 3. How to map back to the individuals? What is the coomand line function used for the above questions? Any help will be appreciated.!! ___ 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] Doubt in the no. of dicom images
Dear All, I use Philips Achieva 3T scanner for the MRI study. When I open the Dicom folder, (say for MPR ) the no. of items I can see is 222 images (IM_xx) for one subject and for other subject, I find it as 166 images. Is it an error in saving the data or the no.of images vary among individuals. Thanks in advance for clarifying my doubt.___ 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] MAking cuts using tksurfer
Dear All, How to explore the cut tools in freesurfer using tksurfer? I'd like to make a cut along the vertex on the cortical surface (say, inflated) to divide medial and lateral components. How to do it after loading DKatlas labels and I want to cut along the vertex to divde medial and lateral components.? Thanks in advance for your response. ___ 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] Merging PArcellation labels
Dear All, Can anyone tell me how to merge the parcellation labels using tksurfer.? For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and caudal middle frontal gyrus. ___ 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.
