Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: recon-all -s -hippo-subfields. But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command less aseg.stats gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm recon-all -s Pat2 \ -i path_to_dicoms/9-2-1.dcm and so on (2) recon-all -s subjid -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio.
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: recon-all -s -hippo-subfields. But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command less aseg.stats gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm recon-all -s Pat2 \ -i path_to_dicoms/9-2-1.dcm and so on (2) recon-all -s subjid -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio are Pat1 and Pat2 etc... different patients? If so, they need to be run separately. e.g. recon-all -s Pat1 -i path to dicoms for patient 1) -all recon-all -s Pat2 -i path to dicoms for patient 2) -all . . . cheers Bruce p.s. for the tcsh bug you should just get your sysadmin to update the version
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hola Eugenio! Thank you so much for quick answer. Well telling from your response it seems that the right way to proceed in order to achieve the absolute volume is to sum up ALL given regions right? And could you please also tell me, which of the hippocampal volumes is the most correct one, the one given primarily by the recon-all or the segmented one? Thank you in advance! Best regards; Cecilio. 2015-05-21 16:54 GMT+08:00 Eugenio Iglesias e.igles...@bcbl.eu: Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: recon-all -s -hippo-subfields. But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command less aseg.stats gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials: (1) recon-all -s Pat1 \ -i path_to_dicoms/9-2-1.dcm recon-all -s Pat2 \ -i path_to_dicoms/9-2-1.dcm and so on (2) recon-all -s subjid -all Part (1) is completed for all my patients and I would like to do part (2) fo r all my patients at the same time. Isn't the right way to procede by typing i n the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi again, - Yes, if you want the whole hippocampal volumes, you can just add all the substructures. - If you compare such volumes with those from aseg.stats, you'll see that they are 10%-15% smaller, but very highly correlated. We have observed that the addition of the 5.3 subfields is a tiny bit better when it comes to separating AD from controls based solely on hippocampal volume, though. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 11:03:04 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hola Eugenio! Thank you so much for quick answer. Well telling from your response it seems that the right way to proceed in order to achieve the absolute volume is to sum up ALL given regions right? And could you please also tell me, which of the hippocampal volumes is the most correct one, the one given primarily by the recon-all or the segmented one? Thank you in advance! Best regards; Cecilio. 2015-05-21 16:54 GMT+08:00 Eugenio Iglesias e.igles...@bcbl.eu : Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: recon-all -s -hippo-subfields. But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command less aseg.stats gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : no, you need to run each subject separately. What I was saying is that you don't need to
Re: [Freesurfer] Motion Correction with T2
Hi Kody, Are you referring to the motion-correction step in recon-all (the one that creates the rawavg.mgz file)? The motion correction in the recon-all step is not really anything that corrects for subject motion and therefore does not deserve it's name. It is rather an avaraging several inputs after aligning them to the first. This is when several T1's are aquired in the same session. For low quality scans this was done to reduce the noise and usually is not necessary any more. In fact I suspect you'd be better off, throwing out the motion corrupted images and using only the best scan. Cheers, Martin On 05/21/2015 11:14 AM, zal...@u.washington.edu wrote: Hello again Freesurfer team, Is it possible to perform a motion correction with only a T1 and a T2 scan, as my lab only has one available T1 scan per participant. Since the intensities of T1 and T2 are opposite of one another I've had no luck so far, but perhaps your team knows of a work-around. Best, Kody J. Zalewski ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] Ventricular aseg error
Hi Freesurfers, I am processing a patient with severe cortical atrophy and exceptionally large ventricles. Reviewing the subcortical segmentation, I found that large volumes within the lateral ventricles were excluded entirely from the aseg file. I checked to see if these volumes were also absent in norm.mgz, but there is no problem with that file. I reran the subcortical segmentation, and met the same issue. Is this a common problem that people run into? I would appreciate any advice to help guide me in troubleshooting this one! Thank you, Devin ___ 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] R: Re: R: Re: Hippo-subfields visualization
Thanks, I have resolved for tksurfer. However, in freeviewer I'm not able visualize correctly the labels of perirhinal and entorhinal in aparc+aseg. Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 21-mag-2015 21.48 A: std...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Hippo-subfields visualization sure, just load the labels into tksurfer or freeview On Thu, 21 May 2015, std...@virgilio.it wrote: Thanks Eugenio. Point A is resolved: some typos in line command.But, I do not found the label of perirhinal in aparc+aseg. Is possible to visualize the enthorhinal, perirhinal and parahippocampus on a surface? Stefano Messaggio originale Da: e.igles...@bcbl.eu Data: 20-mag-2015 23.05 A: std...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Hippo-subfields visualization Hi Stefano, What error do you exactly get when you run the command to visualize the segmentation? If you didn't get any error message, please bear in mind that, because it'd loading a bunch of files simultaneously, it takes a while to load. Regarding B and C: you can extract volumetric masks for cortical structures from the aseg+aparc volume. /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: std...@virgilio.it To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 20, 2015 9:14:05 PM Subject: [Freesurfer] Hippo-subfields visualization Hi list, I'm using version 5.3 and I have performed hippo-subfields analysis. A- I'd like to visualize the mask of each subfield on the T1. In subid/mri, I run the command line above: freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt but I can not visualize the subfields ROI on the T1 B- How I can visualize the entorhinal, perirhinal and parahippocampal on T1 of a subjects? C- I would like to have the ROI entorhinal, perirhinal and parahippocampal for each subject and use it as masks. How can I do? Thanks, Stefano ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3
Hi Eugenio! Thank so much for your time and answers! Best regards; Cecilio. 2015-05-21 17:10 GMT+08:00 Eugenio Iglesias e.igles...@bcbl.eu: Hi again, - Yes, if you want the whole hippocampal volumes, you can just add all the substructures. - If you compare such volumes with those from aseg.stats, you'll see that they are 10%-15% smaller, but very highly correlated. We have observed that the addition of the 5.3 subfields is a tiny bit better when it comes to separating AD from controls based solely on hippocampal volume, though. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 11:03:04 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hola Eugenio! Thank you so much for quick answer. Well telling from your response it seems that the right way to proceed in order to achieve the absolute volume is to sum up ALL given regions right? And could you please also tell me, which of the hippocampal volumes is the most correct one, the one given primarily by the recon-all or the segmented one? Thank you in advance! Best regards; Cecilio. 2015-05-21 16:54 GMT+08:00 Eugenio Iglesias e.igles...@bcbl.eu : Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Cecilio C Baro Perez cecilio.c.b...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: recon-all -s -hippo-subfields. But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command less aseg.stats gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl fis...@nmr.mgh.harvard.edu : Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio.
Re: [Freesurfer] fcseed-sess error
I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta regio_read_register: loading lta RegMat: 0.99848 0.02007 -0.05128 -0.41633; 0.04918 0.09388 0.99437 -30.67201; -0.02477 0.99538 -0.09275 5.35657; 0.0 0.0 0.0 1.0; Label RAS-to-Vox: -0.33283 -0.00669 0.01709 36.13877; 0.00826 -0.33179 0.03092 34.21448; 0.01639 0.03129 0.33146 13.27600; 0.0 0.0 0.0 1.0; PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Computing PVF 27 mri_label2vol done mri_binarize --i /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii --match 1 $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /autofs/cluster/roffman/users/Stable5_PerRun cmdline
Re: [Freesurfer] fcseed-sess error
Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta regio_read_register: loading lta RegMat: 0.99848 0.02007 -0.05128 -0.41633; 0.04918 0.09388 0.99437 -30.67201; -0.02477 0.99538 -0.09275 5.35657; 0.0 0.0 0.0 1.0; Label RAS-to-Vox: -0.33283 -0.00669 0.01709 36.13877; 0.00826 -0.33179 0.03092 34.21448; 0.01639 0.03129 0.33146 13.27600; 0.0 0.0 0.0 1.0; PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Computing PVF 27
[Freesurfer] Motion Correction with T2
Hello again Freesurfer team, Is it possible to perform a motion correction with only a T1 and a T2 scan, as my lab only has one available T1 scan per participant. Since the intensities of T1 and T2 are opposite of one another I've had no luck so far, but perhaps your team knows of a work-around. Best, Kody J. Zalewski ___ 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] funcroi-table-sess error, \set: variable name must begin with a letter\
This is a different error: ERROR: cannot find l_ant_cingulate_allVfix.roicfg On 05/19/2015 02:55 PM, Joseph Andreano wrote: Hi Doug, I'm following up on a thread from a few months back, where we were experiencing difficulty with funcroi-table-sess. (You can find the earlier thread here: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg39326.html) I've attached the dng.log file you requested. Please let me know if you can figure out the problem. Thanks, Joe Andreano _ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _ ___ 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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] TKMEDIT error when SSH'ing
Hi Freesurfer folks I am SSH'ing from one MAC to another. both mac's are running Mac Os 10.6.8 I am ssh'ing with -Y option when I try to run tkmedit I get the error; Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 2763 Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0xacb Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: unknown error code: invalid drawable error: xp_attach_gl_context returned: 2 X Error of failed request: 0 Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 26 (X_GLXMakeContextCurrent) Serial number of failed request: 24 Current serial number in output stream: 24 How can I fix this? Jon ___ 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] Motion Correction with T2
Hi Kody you can use bbregister to register the T2 to the surfaces (and hence the T1) after you have run recon-all. cheers Bruce On Thu, 21 May 2015, zal...@u.washington.edu wrote: Hello again Freesurfer team, Is it possible to perform a motion correction with only a T1 and a T2 scan, as my lab only has one available T1 scan per participant. Since the intensities of T1 and T2 are opposite of one another I've had no luck so far, but perhaps your team knows of a work-around. Best, Kody J. Zalewski ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] fcseed-sess error
Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta regio_read_register: loading lta RegMat: 0.99848 0.02007 -0.05128 -0.41633; 0.04918 0.09388 0.99437 -30.67201; -0.02477 0.99538 -0.09275 5.35657; 0.0 0.0 0.0 1.0; Label RAS-to-Vox: -0.33283 -0.00669 0.01709 36.13877; 0.00826 -0.33179 0.03092 34.21448; 0.01639 0.03129 0.33146 13.27600; 0.0 0.0 0.0 1.0; PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Computing PVF 27 mri_label2vol done mri_binarize --i /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii --match 1 $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /autofs/cluster/roffman/users/Stable5_PerRun cmdline mri_binarize --i /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii --match 1 sysname Linux hostname dauntless machine x86_64 user atanner input /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii frame 0 nErode3d 0 nErode2d 0 output /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/mask.nii
Re: [Freesurfer] R: Re: R: Re: Hippo-subfields visualization
Hi Stefano we need more details than that if you want us to help you. Can you load them into freeview? If so what is wrong with the display? cheers Bruce On Thu, 21 May 2015, std...@virgilio.it wrote: Thanks, I have resolved for tksurfer. However, in freeviewer I'm not able visualize correctly the labels of perirhinal and entorhinal in aparc+aseg. Stefano Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 21-mag-2015 21.48 A: std...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Hippo-subfields visualization sure, just load the labels into tksurfer or freeview On Thu, 21 May 2015, std...@virgilio.it wrote: Thanks Eugenio. Point A is resolved: some typos in line command.But, I do not found the label of perirhinal in aparc+aseg. Is possible to visualize the enthorhinal, perirhinal and parahippocampus on a surface? Stefano Messaggio originale Da: e.igles...@bcbl.eu Data: 20-mag-2015 23.05 A: std...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Hippo-subfields visualization Hi Stefano, What error do you exactly get when you run the command to visualize the segmentation? If you didn't get any error message, please bear in mind that, because it'd loading a bunch of files simultaneously, it takes a while to load. Regarding B and C: you can extract volumetric masks for cortical structures from the aseg+aparc volume. /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: std...@virgilio.it To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 20, 2015 9:14:05 PM Subject: [Freesurfer] Hippo-subfields visualization Hi list, I'm using version 5.3 and I have performed hippo-subfields analysis. A- I'd like to visualize the mask of each subfield on the T1. In subid/mri, I run the command line above: freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt but I can not visualize the subfields ROI on the T1 B- How I can visualize the entorhinal, perirhinal and parahippocampal on T1 of a subjects? C- I would like to have the ROI entorhinal, perirhinal and parahippocampal for each subject and use it as masks. How can I do? Thanks, Stefano ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Delineation of the Retinotopic Visual Areas
Dear Freesufer experts, I may understand some of the .nii.gz files. angle.nii.gz represents the phase of the stimulus and angle.masked.nii.gz was masked by significant map, right? So, angle.nii.gz should be the basis for the delineation,right? Any advice for the delineation would be very appreciated! Mingxia zhang On Wed, May 20, 2015 at 6:15 PM, zhang mingxia zhangmingxia1...@gmail.com wrote: Dear Freesurfer experts, I did the retinotopic mapping analysis followed by https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis and view the results by rtview recommended by you. e.g., for subject s03: rtview --s s03 --rh --polar --real polar/real.nii.gz --imag polar/imag.nii.gz --fsig polar/fsig.nii.gz. rtview seems showing a correct picture with red, blue and green color as other people showed on literature and internet. However, I didn't find a detailed manual for the delineation of the Retinotopic Visual Areas. Hope you guys would answer my basic questions: 1. What's map the delineation based on? In previous email, Doug told me to delineat the boarder of visual area by field sign. However, the value show on the rtview (on the right of map-real-lh.w ) is different from the value of fsig.nii.gz (I loaded it as the overlay and saw two different values in rtview). So, I really wonder what the value of fsig.nii.gz and map-real-lh.w represent? Does one of them represent the degree of the wedge from horizontal which I expected to be the basis of my delineation? 2. Should the delineation be based on the specific value or just the boarder of the color? For example, I firstly want to define V1, How? Do I need to define it based on the specific value showed on rtview? or V1 is always defined on experience of calcarine sulcus and then the boarder of V1 and V2 is defined based on the color change)? Thanks for your always support! Mingxia Zhang ___ 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] Hippocamp subfields
Hi, I am using freesurfer v5.3, can I have hippocamp subfields in this version?? Kind regards ___ 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] R: Re: Hippo-subfields visualization
Thanks Eugenio. Point A is resolved: some typos in line command.But, I do not found the label of perirhinal in aparc+aseg.Is possible to visualize the enthorhinal, perirhinal and parahippocampus on a surface? Stefano Messaggio originale Da: e.igles...@bcbl.eu Data: 20-mag-2015 23.05 A: std...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Hippo-subfields visualization Hi Stefano, What error do you exactly get when you run the command to visualize the segmentation? If you didn't get any error message, please bear in mind that, because it'd loading a bunch of files simultaneously, it takes a while to load. Regarding B and C: you can extract volumetric masks for cortical structures from the aseg+aparc volume. /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: std...@virgilio.it To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 20, 2015 9:14:05 PM Subject: [Freesurfer] Hippo-subfields visualization Hi list, I'm using version 5.3 and I have performed hippo-subfields analysis. A- I'd like to visualize the mask of each subfield on the T1. In subid/mri, I run the command line above: freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt but I can not visualize the subfields ROI on the T1 B- How I can visualize the entorhinal, perirhinal and parahippocampal on T1 of a subjects? C- I would like to have the ROI entorhinal, perirhinal and parahippocampal for each subject and use it as masks. How can I do? Thanks, Stefano ___ 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 ___ 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] R: Re: Hippo-subfields visualization
sure, just load the labels into tksurfer or freeview On Thu, 21 May 2015, std...@virgilio.it wrote: Thanks Eugenio. Point A is resolved: some typos in line command.But, I do not found the label of perirhinal in aparc+aseg. Is possible to visualize the enthorhinal, perirhinal and parahippocampus on a surface? Stefano Messaggio originale Da: e.igles...@bcbl.eu Data: 20-mag-2015 23.05 A: std...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Hippo-subfields visualization Hi Stefano, What error do you exactly get when you run the command to visualize the segmentation? If you didn't get any error message, please bear in mind that, because it'd loading a bunch of files simultaneously, it takes a while to load. Regarding B and C: you can extract volumetric masks for cortical structures from the aseg+aparc volume. /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: std...@virgilio.it To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, May 20, 2015 9:14:05 PM Subject: [Freesurfer] Hippo-subfields visualization Hi list, I'm using version 5.3 and I have performed hippo-subfields analysis. A- I'd like to visualize the mask of each subfield on the T1. In subid/mri, I run the command line above: freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt but I can not visualize the subfields ROI on the T1 B- How I can visualize the entorhinal, perirhinal and parahippocampal on T1 of a subjects? C- I would like to have the ROI entorhinal, perirhinal and parahippocampal for each subject and use it as masks. How can I do? Thanks, Stefano ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fcseed-sess error
What is the voxel size of your functional? 54 is small, but I would expect it to still work. On 05/21/2015 11:20 AM, Alexandra Tanner wrote: Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta regio_read_register: loading lta RegMat: 0.99848 0.02007 -0.05128 -0.41633; 0.04918 0.09388 0.99437 -30.67201; -0.02477 0.99538 -0.09275 5.35657; 0.0 0.0 0.0 1.0; Label RAS-to-Vox: -0.33283 -0.00669 0.01709 36.13877; 0.00826 -0.33179 0.03092 34.21448; 0.01639 0.03129
Re: [Freesurfer] fcseed-sess error
The voxel size for this functional sequence is 3x3x3mm What is the voxel size of your functional? 54 is small, but I would expect it to still work. On 05/21/2015 11:20 AM, Alexandra Tanner wrote: Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta regio_read_register: loading lta RegMat: 0.99848 0.02007 -0.05128 -0.41633; 0.04918 0.09388 0.99437 -30.67201; -0.02477 0.99538 -0.09275 5.35657; 0.0 0.0 0.0 1.0; Label RAS-to-Vox: -0.33283 -0.00669 0.01709 36.13877;
Re: [Freesurfer] fcseed-sess error
I actually already tried rerunning fcseed-config and fcseed-sess lowering the fillthresh (even brought it down to 0) and I still got the same error. I just tried .05 to be thorough but no dice :( Try lowering the fillthreshold to .1 in fcseed-config (means you have to re-run fcseed-sess for all subjects, but see if it makes those two work). For such a small seed, it may even be better to use .05. On 05/21/2015 11:42 AM, Alexandra Tanner wrote: The voxel size for this functional sequence is 3x3x3mm What is the voxel size of your functional? 54 is small, but I would expect it to still work. On 05/21/2015 11:20 AM, Alexandra Tanner wrote: Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -0.3 -0.0 -0.0 36.0; -0.0 -0.0 -0.3 36.0; -0.0 0.3 -0.0 23.5; -0.0 -0.0 -0.0 1.0;
Re: [Freesurfer] fcseed-sess error
Hi Doug, So I just tried making my ROI a little bit bigger in an earlier binarizing step that created my segmentation, and when I ran fcseed-config and fcseed-sess in this same subject it ran without error. I guess it was a sizing issue! Let me know if you have any additional thoughts. Thanks again for your help! Best, Alex I actually already tried rerunning fcseed-config and fcseed-sess lowering the fillthresh (even brought it down to 0) and I still got the same error. I just tried .05 to be thorough but no dice :( Try lowering the fillthreshold to .1 in fcseed-config (means you have to re-run fcseed-sess for all subjects, but see if it makes those two work). For such a small seed, it may even be better to use .05. On 05/21/2015 11:42 AM, Alexandra Tanner wrote: The voxel size for this functional sequence is 3x3x3mm What is the voxel size of your functional? 54 is small, but I would expect it to still work. On 05/21/2015 11:20 AM, Alexandra Tanner wrote: Hi Doug, It is a pretty small segmentation. In subject NNC0931 (the example we're looking at) the segmentation has 54 voxels. fcseed-sess also didn't work in subject NNC0901 -- in that subject the segmentation has 78 voxels. For comparison, in one of the subjects where fcseed-sess completed without error the segmentation has 89 voxels. Do you think this is an issue of size? Thanks! Alex I'm not sure what is going wrong here, but it does not find any voxels when the segmentation is mapped into the functional space. Can you look at /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz And see how many voxels it has? Is it possible that that is a really small segmentation? doug On 05/21/2015 10:30 AM, Alexandra Tanner wrote: Hi Doug and Freesurfers, I'm running fcseed-sess to compute the time course in 12 different ROIs (created with fcseed-config) across 27 subjects. I'm having an issue, however, where fcseed-sess completes for a particular ROI in most subjects but errors out for a few subjects (see log below). I saw someone had the same issue in the mail archives (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-August/032646.html) so I checked the registration but everything seems to look fine. Any other suggestions on how to fix this issue would be greatly appreciated! Thanks! Alex fcseed-config and fcseed-sess commands/logs: # /usr/local/freesurfer/dev/fsfast/bin/fcseed-config -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg -segid 1 -seg lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz -fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat -fsd resting -mean -force # ProjectDir /autofs/cluster/roffman/users/Stable5_PerRun # $Id: fcseed-config,v 1.8 2014/02/25 19:08:31 greve Exp $ # Wed May 20 14:03:50 EDT 2015 fcname lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.dat fsd resting segstem lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol RegDOF 6 FillThresh .5 DoMean 1 DoSVD 0 DoSqr 0 MakeMask 0 WMErode 0 SVDSynth 0 DoWM 0 UseB0DC 0 segidlist 1 Tue May 19 17:40:27 EDT 2015 Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/dev/fsfast/bin/fcseed-sess -s NNC0931 -cfg /cluster/roffman/users/Stable5_PerRun/FC_Analyses/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.cfg freesurfer-Linux-centos6_x86_64-dev-20150519 mri_label2vol --seg /cluster/roffman/users/Stable5_PerRun/NNC0931/mri/lh_7Network_6_FPCN_inferiorparietal_supramarginal_Vtx126184_sm04.bin.vol.mgz --reg /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta --temp /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii --fillthresh .5 --o /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii --pvf /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii PVF /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/pvf.nii Number of labels: 0 Annot File: (null) Template Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/template.nii Outut Volume: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/tmp.fcseed-sess.7514/seg.nii Registration File: /autofs/cluster/roffman/users/Stable5_PerRun/NNC0931/resting/014/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv
Re: [Freesurfer] TKMEDIT error when SSH'ing
Have you verified that the machine you are ssh'ing into will display tkmedit even if you are not ssh'ing into it? I ask because OSX 10.6 is an end-of-life operating system and that error is usually associated with incompatible graphics card. However, even if it did work while sitting at the host machine, I have never been able to successfully perform X Forwarding over ssh from one Mac to another Mac when using the tktools, or any graphical tools that I can recall for that matter. -Zeke Hi Freesurfer folks I am SSH'ing from one MAC to another. both mac's are running Mac Os 10.6.8 I am ssh'ing with -Y option when I try to run tkmedit I get the error; Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 2763 Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: kCGErrorIllegalArgument: CGSSetWindowSendExposed: Invalid window 0xacb Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] Error: unknown error code: invalid drawable error: xp_attach_gl_context returned: 2 X Error of failed request: 0 Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 26 (X_GLXMakeContextCurrent) Serial number of failed request: 24 Current serial number in output stream: 24 How can I fix this? Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Upgrading Software
Hello, Is there any detailed information on the possible differences in results wwhen upgrading to the latest FreeSurfer software? As it pertains to the scans already processed with old software compared to any scans processed with a newer version of the software. Can I install the new version of Freeview without the new version of FreeSurfer? Would there be any differences to between scans corrected before and after upgrade? I cannot seem to get the 'curl -O' to download the software. Are there any troubleshooting methods to this? Testing the harvard ftp server also fails. Has it been down? Thank you so much, Joseph ___ 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] Custom LookUp Table
I would like to view just the hippocampus in the aseg.mgz file overlaid with the brain.mgz. I created a custom lookup table by commenting all entries except 0 (Unknown) and 17 (Left-Hippocampus). See below for a snippet of the lookup table. When I load this LookUp table I see numerous structures (7, 8, 10, 12, 13, 14, 41, 47, 51) all labeled with various shades of yellow. Any idea why this is happening? What am I doing wrong? Bob #No. Label Name:R G B A # 0 Unknown 0 0 0 0 ... # 16 Brain-Stem 119 159 176 0 17 Left-Hippocampus220 216 20 0 # 18 Left-Amygdala … ___ 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] Upgrading Software
Hello, Is there any detailed information on the possible differences in results wwhen upgrading to the latest FreeSurfer software? As it pertains to the scans already processed with old software compared to any scans processed with a newer version of the software. When freesurfer6.0 is released we will publish a set of brain maps for some of our internal data sets which will show the regions of the brain that demonstrate statistical differences for various measures (e.g. thickness, area) between the most recent release v5.3 and the upcoming release v6.0. Whether your data will exhibit the same trends is impossible to say. But we do make the following statement on our download page in regards to processing subjects with freesurfer: *Important Note!* When processing a group of subjects for your study, it is essential to process all your subjects with the same version of freesurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms (for instance the 32b and 64b CentOS 4 builds should produce identical results), there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). Can I install the new version of Freeview without the new version of FreeSurfer? Would there be any differences to between scans corrected before and after upgrade? Yes, you can install the new version of freeview over your existing version of freeview as updates to that application, and edits made with it, should not effect to overall processing stream. Just follow the Freeview dev version download instructions on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download I cannot seem to get the 'curl -O' to download the software. Are there any troubleshooting methods to this? Testing the harvard ftp server also fails. Has it been down? I just tested the following commands on my home network and they both worked for me. $ curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg $ curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview.zip -Zeke Thank you so much, Joseph ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
