[Freesurfer] conflicting Monte Carlo simulation results...
Dear Freesurfer experts: I ran into a confusing problem when applying Monte Carlo simulation to control for multiple comparisons. I am using the buckner data from tutorial dataset. I first tried the simulation based on Freesurfer;s 2012 manual: (http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-2012.pdf) mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite This produced a "mc-z.negative.sig.cluster.summary". In this text, no clusters survived correction. Later on, I applied on a slightly different script, based on Freesurfer tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons) mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces It produced a "cache.th40.neg.sig.cluster.summary" this time. But according to this result, 22 clusters survived. Now I am quite confused, because both corrections have the same voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the drastic discrepancies come from and which result is more reliable? Many thinks in advance. Best, Karl ___ 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] The name of regions of annotation file issue viewing by tksurfer
Hi Thank you so much for your help. I just got your meaning. I created new LUT file by just changing randomly the RBG values for each 13 specific regions and opened the annot file in tksurfer. And the strange issue is that just for paracentral I used your values I had paracentral in tksurfer GUI name, but for the rest of the regions I saw that problem I had before! (the region's names were not the names in .ctab file). So, what do you think about? Regards, Faeze On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. sorry, I could not understand what you mean. > How you found 23 230 60 values for paracentral region? I mean. Are these > from Freesurfer LUT? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei > wrote: > >> Thank you for your response. It is better to explain my question that the >> coordinates for paracentral in .ctab file is '63 100 60', that you changed >> these to '23 230 60' in your new version. My question is that how you >> applied such this change on the RBG values for this region? >> >> Regards, >> Faezeh >> >> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei >> wrote: >> >>> Thank you so much for you response. I should say that I know about what >>> you are saying. My issue is that I have these 4 columns in my LUT file. Why >>> and how can I change the numbers (RGB values) to create new LUT? >>> >>> Bests, >>> Faezeh >>> >>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei >>> wrote: >>> Hi, Thank you so much for you descriptions. I checked out the link you just sent me. Because I do not have many experiences working with Freesurfer, I really could not understand about how I can do such this revising in LUT file. Can you explain more about this? I truly appreciate your time and help. Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: > Hi, > > I really appreciate you for help me in this process. May you clarify > me from which pattern you changed the RGB values for that region? How I > can > change the coordinates for the others? > > Regards, > Faezeh Vedaei > > > On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei > wrote: > >> Hi, >> >> I should let you know that, it works! It shows paracentral name in >> tksurfer. So, how I have to revise my .ctab file to get the right result? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> Thank you for your response. I just used the command you suggested >>> to use by just a change in calling .ctab LUT file. I used the path: >>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by >>> just >>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file >>> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >>> opinion? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >> > wrote: >>> Hi, Here is the text format of those files. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei < faezeved...@gmail.com> wrote: > Hi > > Thank you so much for your response. I attached here three files > including the command lines, LUT file , and the list of names I want > to get > and what the result is actually. I'd appreciate if you look at them > and let > me know what is wrong with that. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei < > faezeved...@gmail.com> wrote: > >> Hi, >> >> I checked again to arrange the labels in the order of LUT file, >> but the result has not changed. Can you help me more how I can fix >> this >> problem? Thank you so much for your time and help. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei < >> faezeved...@gmail.com> wrote: >> >>> Hi, >>> >>> Thank you for your response. Yes, you are right. The names come >>> from the color LUT file. But, the issue is that I chose the label >>> files >>> from that LUT file too. It meas the source that I chose the label >>> files >>> from and the source of the region's names in tksurfer are the same. >>> The >>> problem is just I do not have the label's names I merged to create >>> annot >>> file, in the tksurfer GUI. It shows another names of that list! So,
Re: [Freesurfer] Topological White Matter Correction
Hi Kiersten the topology correction algorithm is this one: http://www.ncbi.nlm.nih.gov/pubmed/11293693 cheers Bruce On Wed, 2 Mar 2016, Kiersten Snyder wrote: Hello FreeSurfer Experts,What image processing technique is behind the Topological White Matter Correction to correct topological defects? Is it true that FreeSurfer take into account your edits as a "suggestion" and incorporates into some type of algorithm? I would like to have a more thorough understanding of the image processing that this function utilizes. Thanks for the help! Kiersten ___ 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] hippocampus subfields
Sweet, just what I wanted. Thank you, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias Sent: Wednesday, March 2, 2016 2:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampus subfields OK now I get it ;-) You can simply do: mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl [lr]h.hippoSfLabels-T1-T2.v10.mgz The rl flag says: "reslice like the following volume" 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 From: "Prabesh Kanel" To: "Freesurfer support list" Sent: Wednesday, March 2, 2016 8:31:17 PM Subject: Re: [Freesurfer] hippocampus subfields Hi Eugenio, Thank you, for your quick reply. It has happened to me in 4% of the cases, but my data sample is small like 100 data points. Addition to the second question: When I segment the hippocampus, I get the discrete segmentation volume at 0.333 mm resolution in the file [lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each voxel is labelled based on the subfield. I can use mri_extract_label or mri_binarize to extract individual subfield. But this segmentation will have voxels with the original label. If I load the file along with the T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the intensities at this place, I believe the intensity value is from T2.FSspace.mgz. Are those intensities values different from the original T2 images? If not, Is it possible to get those value at each voxel location? Best Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias Sent: Wednesday, March 2, 2016 12:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampus subfields Hi Prabesh, I think this is due to a bug that I found recently and which I'm trying to track down. Has it happened to you with many scans? The failure rate is less than 1% in my data. Regarding your second question: I'm sure it's not too trivial ;-) but I don't understand exactly what you mean. Do you want to deform the segmentations back to the original T2 space? 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 From: "Prabesh Kanel" To: "Freesurfer support list" Sent: Wednesday, March 2, 2016 6:07:13 PM Subject: [Freesurfer] hippocampus subfields Freesurfer List, I ran recon-all to segment hippocampus subfield using the development version of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and T2 images. But for some of the scans, the process stops at a point and doesn't seem to progress further. That happens in only a few cases and only when the data are run using the flag -hippocampal-subfields-T1T2. I have attached a log file of one of the case in this email. Another query that I have is to get T2 segmented subfields images (one with intensity values rather than labels). Is there an easier way to get T2 subfields segmented images using the segmentation volumes and T2.FSspace.mgz. Sorry, if this question seems too trivial. Regards, Prabesh ___ 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 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 ht
[Freesurfer] Topological White Matter Correction
Hello FreeSurfer Experts, What image processing technique is behind the Topological White Matter Correction to correct topological defects? Is it true that FreeSurfer take into account your edits as a "suggestion" and incorporates into some type of algorithm? I would like to have a more thorough understanding of the image processing that this function utilizes. Thanks for the help! Kiersten ___ 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] Unknown option DKTatlas40
It appears to be an issue with the dev build and should be fixed in tomorrows build. -Zeke On 03/02/2016 08:31 AM, Watson, Christopher wrote: > The option should be: > --annot aparc.DKTatlas40 > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman > [marmaduke.wood...@univ-amu.fr] > Sent: Wednesday, March 2, 2016 08:27 > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Unknown option DKTatlas40 > > hi > > I'm using the dev version of FreeSurfer on 64-bit Fedora 23. > > > Recon-all runs fine but at the end I see > > $ recon-all -s tvb -aparc2aseg > ... >mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40 > > ERROR: Option --DKTatlas40 unknown > > > Running that command > > $ mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos > > without the --DKTatlas40 appears to run correctly. > > > Is this just an issue with the dev version or have I done something silly? > > > thanks, > Marmaduke > > > ps bugr output > > FREESURFER_HOME: /opt/freesurfer > > Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160229 > > RedHat release: Fedora release 23 (Twenty Three) > > Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64 > > ___ > 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] The name of regions of annotation file issue viewing by tksurfer
just change the values and re-run with different numbers and see what happens On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. sorry, I could not understand what you mean. > How you found 23 230 60 values for paracentral region? I mean. Are these > from Freesurfer LUT? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei wrote: >> >> Thank you for your response. It is better to explain my question that the >> coordinates for paracentral in .ctab file is '63 100 60', that you changed >> these to '23 230 60' in your new version. My question is that how you >> applied such this change on the RBG values for this region? >> >> Regards, >> Faezeh >> >> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei >> wrote: >>> >>> Thank you so much for you response. I should say that I know about what >>> you are saying. My issue is that I have these 4 columns in my LUT file. Why >>> and how can I change the numbers (RGB values) to create new LUT? >>> >>> Bests, >>> Faezeh >>> >>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei >>> wrote: Hi, Thank you so much for you descriptions. I checked out the link you just sent me. Because I do not have many experiences working with Freesurfer, I really could not understand about how I can do such this revising in LUT file. Can you explain more about this? I truly appreciate your time and help. Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: > > Hi, > > I really appreciate you for help me in this process. May you clarify me > from which pattern you changed the RGB values for that region? How I can > change the coordinates for the others? > > Regards, > Faezeh Vedaei > > > On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei > wrote: >> >> Hi, >> >> I should let you know that, it works! It shows paracentral name in >> tksurfer. So, how I have to revise my .ctab file to get the right result? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> Thank you for your response. I just used the command you suggested to >>> use by just a change in calling .ctab LUT file. I used the path: >>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by >>> just >>> calling aparc.annot.a2009s.ctab. It is strange that I created annot >>> file for >>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >>> opinion? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >>> wrote: Hi, Here is the text format of those files. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > > Hi > > Thank you so much for your response. I attached here three files > including the command lines, LUT file , and the list of names I want > to get > and what the result is actually. I'd appreciate if you look at them > and let > me know what is wrong with that. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei > wrote: >> >> Hi, >> >> I checked again to arrange the labels in the order of LUT file, >> but the result has not changed. Can you help me more how I can fix >> this >> problem? Thank you so much for your time and help. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> Thank you for your response. Yes, you are right. The names come >>> from the color LUT file. But, the issue is that I chose the label >>> files from >>> that LUT file too. It meas the source that I chose the label files >>> from and >>> the source of the region's names in tksurfer are the same. The >>> problem is >>> just I do not have the label's names I merged to create annot file, >>> in the >>> tksurfer GUI. It shows another names of that list! So, what do you >>> think >>> about? What is the problem? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >>> wrote: Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Hi, Thank you for your response. sorry, I could not understand what you mean. How you found 23 230 60 values for paracentral region? I mean. Are these from Freesurfer LUT? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei wrote: > Thank you for your response. It is better to explain my question that the > coordinates for paracentral in .ctab file is '63 100 60', that you changed > these to '23 230 60' in your new version. My question is that how you > applied such this change on the RBG values for this region? > > Regards, > Faezeh > > On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei > wrote: > >> Thank you so much for you response. I should say that I know about what >> you are saying. My issue is that I have these 4 columns in my LUT file. Why >> and how can I change the numbers (RGB values) to create new LUT? >> >> Bests, >> Faezeh >> >> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> Thank you so much for you descriptions. I checked out the link you just >>> sent me. Because I do not have many experiences working with Freesurfer, I >>> really could not understand about how I can do such this revising in LUT >>> file. Can you explain more about this? I truly appreciate your time and >>> help. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei >>> wrote: >>> Hi, I really appreciate you for help me in this process. May you clarify me from which pattern you changed the RGB values for that region? How I can change the coordinates for the others? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei wrote: > Hi, > > I should let you know that, it works! It shows paracentral name in > tksurfer. So, how I have to revise my .ctab file to get the right result? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei > wrote: > >> Hi, >> >> Thank you for your response. I just used the command you suggested to >> use by just a change in calling .ctab LUT file. I used the path: >> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by >> just >> calling aparc.annot.a2009s.ctab. It is strange that I created annot file >> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >> opinion? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> >>> Here is the text format of those files. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei >> > wrote: >>> Hi Thank you so much for your response. I attached here three files including the command lines, LUT file , and the list of names I want to get and what the result is actually. I'd appreciate if you look at them and let me know what is wrong with that. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei < faezeved...@gmail.com> wrote: > Hi, > > I checked again to arrange the labels in the order of LUT file, > but the result has not changed. Can you help me more how I can fix > this > problem? Thank you so much for your time and help. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei < > faezeved...@gmail.com> wrote: > >> Hi, >> >> Thank you for your response. Yes, you are right. The names come >> from the color LUT file. But, the issue is that I chose the label >> files >> from that LUT file too. It meas the source that I chose the label >> files >> from and the source of the region's names in tksurfer are the same. >> The >> problem is just I do not have the label's names I merged to create >> annot >> file, in the tksurfer GUI. It shows another names of that list! So, >> what do >> you think about? What is the problem? >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei < >> faezeved...@gmail.com> wrote: >> >>> Hi Freesurfer experts, >>> >>> I have created an annotation file by several label files using >>> mris_label2annot command in Freesurfer. The problem is that when I >>> open >>> this annot file in tksurfer and click on colored regions which >>> corresponded >>> to specific labels I had chosen them, I do not have their name on >>> the >>> vertex information part at
Re: [Freesurfer] hippocampus subfields
OK now I get it ;-) You can simply do: mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl [lr]h.hippoSfLabels-T1-T2.v10.mgz The rl flag says: "reslice like the following volume" 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 From: "Prabesh Kanel" To: "Freesurfer support list" Sent: Wednesday, March 2, 2016 8:31:17 PM Subject: Re: [Freesurfer] hippocampus subfields Hi Eugenio, Thank you, for your quick reply. It has happened to me in 4% of the cases, but my data sample is small like 100 data points. Addition to the second question: When I segment the hippocampus, I get the discrete segmentation volume at 0.333 mm resolution in the file [lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each voxel is labelled based on the subfield. I can use mri_extract_label or mri_binarize to extract individual subfield. But this segmentation will have voxels with the original label. If I load the file along with the T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the intensities at this place, I believe the intensity value is from T2.FSspace.mgz. Are those intensities values different from the original T2 images? If not, Is it possible to get those value at each voxel location? Best Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias Sent: Wednesday, March 2, 2016 12:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampus subfields Hi Prabesh, I think this is due to a bug that I found recently and which I'm trying to track down. Has it happened to you with many scans? The failure rate is less than 1% in my data. Regarding your second question: I'm sure it's not too trivial ;-) but I don't understand exactly what you mean. Do you want to deform the segmentations back to the original T2 space? 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 From: "Prabesh Kanel" To: "Freesurfer support list" Sent: Wednesday, March 2, 2016 6:07:13 PM Subject: [Freesurfer] hippocampus subfields Freesurfer List, I ran recon-all to segment hippocampus subfield using the development version of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and T2 images. But for some of the scans, the process stops at a point and doesn't seem to progress further. That happens in only a few cases and only when the data are run using the flag -hippocampal-subfields-T1T2. I have attached a log file of one of the case in this email. Another query that I have is to get T2 segmented subfields images (one with intensity values rather than labels). Is there an easier way to get T2 subfields segmented images using the segmentation volumes and T2.FSspace.mgz. Sorry, if this question seems too trivial. Regards, Prabesh ___ 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 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] hippocampus subfields
Hi Eugenio, Thank you, for your quick reply. It has happened to me in 4% of the cases, but my data sample is small like 100 data points. Addition to the second question: When I segment the hippocampus, I get the discrete segmentation volume at 0.333 mm resolution in the file [lr]h.hippoSfLabels-T2.v10.mgz and [lr]h.hippoSfLabels-T1-T2.v10.mgz . Each voxel is labelled based on the subfield. I can use mri_extract_label or mri_binarize to extract individual subfield. But this segmentation will have voxels with the original label. If I load the file along with the T2.FSspace.mgz in Freeview, I can hover my mouse to a location and get the intensities at this place, I believe the intensity value is from T2.FSspace.mgz. Are those intensities values different from the original T2 images? If not, Is it possible to get those value at each voxel location? Best Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias Sent: Wednesday, March 2, 2016 12:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampus subfields Hi Prabesh, I think this is due to a bug that I found recently and which I'm trying to track down. Has it happened to you with many scans? The failure rate is less than 1% in my data. Regarding your second question: I'm sure it's not too trivial ;-) but I don't understand exactly what you mean. Do you want to deform the segmentations back to the original T2 space? 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 From: "Prabesh Kanel" To: "Freesurfer support list" Sent: Wednesday, March 2, 2016 6:07:13 PM Subject: [Freesurfer] hippocampus subfields Freesurfer List, I ran recon-all to segment hippocampus subfield using the development version of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and T2 images. But for some of the scans, the process stops at a point and doesn't seem to progress further. That happens in only a few cases and only when the data are run using the flag -hippocampal-subfields-T1T2. I have attached a log file of one of the case in this email. Another query that I have is to get T2 segmented subfields images (one with intensity values rather than labels). Is there an easier way to get T2 subfields segmented images using the segmentation volumes and T2.FSspace.mgz. Sorry, if this question seems too trivial. Regards, Prabesh ___ 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] hippocampus subfields
Hi Prabesh, I think this is due to a bug that I found recently and which I'm trying to track down. Has it happened to you with many scans? The failure rate is less than 1% in my data. Regarding your second question: I'm sure it's not too trivial ;-) but I don't understand exactly what you mean. Do you want to deform the segmentations back to the original T2 space? 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 From: "Prabesh Kanel" To: "Freesurfer support list" Sent: Wednesday, March 2, 2016 6:07:13 PM Subject: [Freesurfer] hippocampus subfields Freesurfer List, I ran recon-all to segment hippocampus subfield using the development version of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and T2 images. But for some of the scans, the process stops at a point and doesn't seem to progress further. That happens in only a few cases and only when the data are run using the flag -hippocampal-subfields-T1T2. I have attached a log file of one of the case in this email. Another query that I have is to get T2 segmented subfields images (one with intensity values rather than labels). Is there an easier way to get T2 subfields segmented images using the segmentation volumes and T2.FSspace.mgz. Sorry, if this question seems too trivial. Regards, Prabesh ___ 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] Problem with mriconvert
Hello, We are medicine students who are using freesurfer for research. We had been using freesurfer in Ubuntu 12.02 without encountering any trouble; recently we updated to 14.04. Now, when we attempt to convert a mgz file to nii using mriconvert, we have an error regarding failure to write the files .nii The command we are using is as follows: mri_convert ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.mgz ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_ cortical_seg.nii The error message we find is this one: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/psa/datos_MRI_cerebral/estructural/Freesurfer_seg_cortical_resultado/C2090_cortical_seg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.74975e-08, 0) j_ras = (0, 0, -1) k_ras = (1.21072e-08, 1, 0) writing to ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii... niiWrite(): error opening file ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii ERROR: failure writing ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii We really could use your help, since we can't find any solution in the Internet. Thanks in advance for your attention. Regards, Óscar and Alba ___ 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] Deflate surface
Hi I would like to resample the cortical surface on the sphere at a lower resolution, and then deflate the surface to its folded form. Is this something which can be done using the inflated surface that FS generates? Thank you, Marmaduke ___ 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] Unknown option DKTatlas40
The option should be: --annot aparc.DKTatlas40 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman [marmaduke.wood...@univ-amu.fr] Sent: Wednesday, March 2, 2016 08:27 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unknown option DKTatlas40 hi I'm using the dev version of FreeSurfer on 64-bit Fedora 23. Recon-all runs fine but at the end I see $ recon-all -s tvb -aparc2aseg ... mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40 ERROR: Option --DKTatlas40 unknown Running that command $ mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos without the --DKTatlas40 appears to run correctly. Is this just an issue with the dev version or have I done something silly? thanks, Marmaduke ps bugr output FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160229 RedHat release: Fedora release 23 (Twenty Three) Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64 ___ 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] mysterious fsgd format error (not the end of line problem)
No worries, it happens to all of us Bruce > On Mar 2, 2016, at 12:20 AM, Joseph Dien wrote: > > Oops, never mind. User error. I’m too embarrassed to even explain what I > did. :) > > Joe > >> On Feb 29, 2016, at 21:38, Joseph Dien wrote: >> >> Hi, >> I’m having an fsgd error that has totally stumped me. I’m trying to run >> the following command to compute the second level statistics: >> >> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz --nii.gz >> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C >> normAcc.mtx >> >> I get the error message: >> >> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white >> gdfReadHeader: reading RPA-accGT.fsgd >> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title >> >> I used the utility flip to make sure the file was in UNIX format (with >> linefeeds). >> I then double-checked by reading in the binary codes with Matlab’s fread and >> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed). >> >> Here is the contents of the fsgd file. >> >> GroupDescriptorFile 1 >> Title RP1 >> Class Main >> Variables LogoAcc NormAcc OrthAcc PhonAcc >> InputRPA903 Main0.750.790.770.62 >> InputRPA906 Main0.810.810.830.74 >> InputRPA907 Main0.871 0.840.83 >> InputRPA908 Main0.910.930.950.89 >> InputRPA909 Main0.740.950.720.72 >> InputRPA910 Main0.850.960.810.79 >> InputRPA912 Main0.750.780.730.73 >> InputRPA914 Main0.7 0.850.830.81 >> InputRPA915 Main0.850.890.750.83 >> InputRPA916 Main0.840.920.870.72 >> InputRPA917 Main0.830.930.920.83 >> InputRPA918 Main0.870.910.790.85 >> InputRPA919 Main0.860.960.910.88 >> InputRPA920 Main0.840.920.870.84 >> InputRPA921 Main0.870.920.880.85 >> InputRPA922 Main0.8 0.9 0.9 0.72 >> >> What’s really driving me to distraction is that a previous version of this >> file (with a different set of participants) works fine. I’m attaching both. >> RPA-accGT.fsgd does not work and RPA-acc.fsgd does work. Using Matlab’s >> fread, the first 85 characters (first four lines) of both files are >> identical. >> >> I’m running on OS X 10.11.3. I’m using FSFAST 5.20. Matlab 2015b. >> >> Any help would be greatly appreciated! >> >> Joe >> >> >> >> >> Joseph Dien, PhD >> Senior Research Scientist >> Maryland Neuroimaging Center >> University of Maryland, College Park >> E-mail: jdie...@mac.com >> Cell Phone: 202-297-8117 >> http://joedien.com >> >> ___ >> 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. > > > > Joseph Dien, PhD > Senior Research Scientist > Maryland Neuroimaging Center > University of Maryland, College Park > E-mail: jdie...@mac.com > Cell Phone: 202-297-8117 > http://joedien.com > > ___ > 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.