Re: [Freesurfer] Difference in GMV generated from qdec and mris_anatomical_stats
Dear All, Sorry for this email. I think I made some mistakes. When I redone the analysis, the values were same. Kindly ignore the email. From: Anupa AV av.an...@yahoo.com To: Freesurfer freesurfer@nmr.mgh.harvard.edu; Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Thursday, October 3, 2013 11:06 AM Subject: Difference in GMV generated from qdec and mris_anatomical_stats Dear FS experts, I was trying to find the gray matter volume of superior temporal gyrus (STG) for schizophrenia patients using freesurfer. I ran recon-all and generated the rh/lh.aparc.volume.stats using qdec. From that, I got the volume for left hand lh_superiortemporal_volume,=11893. Out of curiosity, I separately found the STG volume for this patient alone using the follo. steps. 1. Saved the label lh.STG using tksurfer -annot aparc SZ01 lh pial 2. Then generated the volume using mris_anatomical_stats. 3. I found the value to be 16268. I'm wondering why there is so much changes in the generation of GM volumes. Can anyone please help me with my query?___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] missing eTIV in asegstats2table
Hi, Thanks Marcos for your reply. My problem is that asegstats2table does not output values for eTIV. I do not manage to figure out why. But maybe your script could work. Anyone knows what is the corresponding FieldName Index for eTIV?? I checked a aseg.stats file and did not find it. Thanks a lot Dani Message: 7 Date: Wed, 02 Oct 2013 10:32:51 -0300 From: Marcos Martins da Silva marc...@hucff.ufrj.br Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: Daniel Ferreira dani...@ull.es Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 1380720771.1845.9.camel@alien Content-Type: text/plain; charset=utf-8 You can use in a loop with your subjects. It extracts the fields I want and some others including the etiv to a table named AsegVol. You may change the number of the fields to get what you need. The code I am sending you addresses hippocampus, putamen and caudate (both sides). for i in $(ls -d suj*) do asegstats2table --segno 11 12 17 50 51 53 -s $i --tablefile AsegVol done Notice that suj is the prefix of all my subjects in freesurfer/subjects folder I hope it helps you. Em Qua, 2013-10-02 ___ 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] Effects of age on different parameters (thickness, lGI...)
Hi Doug, I´m a bit unsure about polynomial fitting with qdec. So I want to demonstrate linear, quadratic and cubic effects of age on lGI. You wrote: If you need to test all 3, then you'll have to use mri_glmfit with and FSGD file. I want to be sure if it is correct to demonstrate: 1. age linear effects: age linear (for example 12 Years) as continous (covariate)? 2. age quadratic effects: age square (144 Years) as continous (covariate) and age linear (12 Years) as nuisance variable? 3. age cubic effects: age cubic (1728 Years) as continous (covariate) and age linear (12 years) as nuisance variable? Is it neccesary to include age square (144 years) in the model to show only the cubic effects? And if it is neccesary do I need mri_glmfit with a FSGD file or can I add age square (144 Years) as a seocond nuisance variable in qdec? Best wishes and thanks a lot Daniel ___ 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: Fwd: V1 label
Hi Krista I've never seen that happen before. Can you upload this subject and we will take a look? thanks Bruce On Wed, 2 Oct 2013, krista kelly wrote: Hi Bruce, I've tried twice to post this to the freesurfer mail list but it hasn't worked, I'm assuming because of the attached pictures. I'm going to try this again with only one picture and see if it works. I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well. Here are the commands I ran: recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.nii.gz By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left hemisphere with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer. Is there something I'm doing wrong? Please let me know you're not able to see the snapshots. Thanks! Krista On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Krista, which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce On Mon, 23 Sep 2013, krista kelly wrote: Hi all, I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below). Thanks! Hi Doug, Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below: recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz then recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead? Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much. Thanks! On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: How did you do the transfer? What was your cmd line? doug On 09/10/2013 05:31 PM, krista kelly wrote: Hello, I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow? I've attached a picture to show as an example. Please let me know if the picture cannot be viewed. Thanks! Krista ___ 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:
Re: [Freesurfer] Hippocampal subfield segmentation paused
Hi, Eugenio, I have already sent the log files to you. And would you please give me a hint what is the right command for computing subfields with high-res T2? Thank you very much!! -Irene From: Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu To: Irene Lee lee.iren...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 1, 2013 4:37 PM Subject: Re: [Freesurfer] Hippocampal subfield segmentation paused Hi Irene, two things: 1. Can you please send us the log files of the recon? 2. The command you executed will compute the subfield segmentation based only on the T1, not the high-res T2. Cheers, /Eugenio On 10/01/2013 04:30 PM, Irene Lee wrote: Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the command recon-all -s my subject -all -hippo-subfields It was running well, however, it halted/paused after it displayed the following information:final transformation (x=..,yr=..,zr=..) and a 4x4 matrix. For a week it is not going anywhere and not producing any output. The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer. Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!! -Irene ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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] Hippocampal subfield segmentation paused
Hi again, Irene, On 10/03/2013 09:39 AM, Irene Lee wrote: Hi, Eugenio, I have already sent the log files to you. Sorry, I should have been more specific. I meant [subject_dir]/scripts/recon-all.log and [subject_dir]/scripts/hippo-subfields.log And would you please give me a hint what is the right command for computing subfields with high-res T2? Thank you very much!! This is not an option at this point, but we are working on it. Cheers, /Eugenio -Irene *From:* Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu *To:* Irene Lee lee.iren...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, October 1, 2013 4:37 PM *Subject:* Re: [Freesurfer] Hippocampal subfield segmentation paused Hi Irene, two things: 1. Can you please send us the log files of the recon? 2. The command you executed will compute the subfield segmentation based only on the T1, not the high-res T2. Cheers, /Eugenio On 10/01/2013 04:30 PM, Irene Lee wrote: Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the command recon-all -s my subject -all -hippo-subfields It was running well, however, it halted/paused after it displayed the following information:final transformation (x=..,yr=..,zr=..) and a 4x4 matrix. For a week it is not going anywhere and not producing any output. The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer. Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!! -Irene ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com http://www.jeiglesias.com/ igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] Repost: pcc maps and mri_glmfit
Hi Doug, when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit. I am not sure why this is happening. In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those? Thanks, Caspar 2013/10/1 Douglas N Greve gr...@nmr.mgh.harvard.edu On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote: Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? I just run a t-test of the r-values. I don't have a program to convert them to z-values, however, there are z-values that are created in the first level analysis. These are generated from the p-values but I bet it would give you the same thing. Use -m z with isxconcat-sess if you want to use the z. *Is the average r-value or z-value saved somewhere? Which level? For mri_glmfit, they are not, but it is not hard to get them with matlab. *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? Not usually, but it could be done by not including -no-whiten when you run mkanalysis-sess. I usually use the regression coefficients instead of correlation coefficients because that they are at least unbiased with respect to noise level and autocorrelation. doug I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar ___ 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 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] LGI longitudinal data
Hi Tricia, try recon-all -long subject001 subject001_base -localGI Best, Martin On 09/28/2013 01:53 PM, Tricia Merkley wrote: Hi, Is it possible to run the LGI on data that has already been longitudinally processed? For example, when I try to run: recon-all -s subject001.long.subject001_base -localGI I get the following error: ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long tpNid templateid \' where tpNid is the time point id (SAME as cross sectional ID) and templateid is the ID created in the -base run. The directory tpNid.long.templateid will be created automatically or used for output, if it already exists. This is using v5.1.0, and no, I'm not trying to re-run a longitudinal time point. Just the LGI. I'd appreciate any suggestions! Thanks so much, Tricia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT 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.
Re: [Freesurfer] missing eTIV in asegstats2table
Hi Dani, etiv is in the header, not in the table where the individual strucures are) and looks like this: # Measure IntraCranialVol, ICV, Intracranial Volume, 1736177.143497, mm^3 asegstats2table grabs it also. Best, Martin On 10/03/2013 04:54 AM, Daniel Ferreira wrote: Hi, Thanks Marcos for your reply. My problem is that asegstats2table does not output values for eTIV. I do not manage to figure out why. But maybe your script could work. Anyone knows what is the corresponding FieldName Index for eTIV?? I checked a aseg.stats file and did not find it. Thanks a lot Dani Message: 7 Date: Wed, 02 Oct 2013 10:32:51 -0300 From: Marcos Martins da Silva marc...@hucff.ufrj.br mailto:marc...@hucff.ufrj.br Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: Daniel Ferreira dani...@ull.es mailto:dani...@ull.es Cc:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 1380720771.1845.9.camel@alien mailto:1380720771.1845.9.camel@alien Content-Type: text/plain; charset=utf-8 You can use in a loop with your subjects. It extracts the fields I want and some others including the etiv to a table named AsegVol. You may change the number of the fields to get what you need. The code I am sending you addresses hippocampus, putamen and caudate (both sides). for i in $(ls -d suj*) do asegstats2table --segno 11 12 17 50 51 53 -s $i --tablefile AsegVol done Notice that suj is the prefix of all my subjects in freesurfer/subjects folder I hope it helps you. Em Qua, 2013-10-02 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT 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] LGi computation on computer cluster
Hio We want to compute the LGI index, using our local computing cluster. the cluster does not have matlab or it's image processing toolbox on the computing nodes. Which matlab .m files does the LGI computation use? Thanks -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ 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] trouble with pial surface in v5.1
Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar attachment: inhom.png___ 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] trouble with pial surface in v5.1
Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar ___ 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] trouble with pial surface in v5.1
Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)? Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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] trouble with pial surface in v5.1
is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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
Re: [Freesurfer] Repost: pcc maps and mri_glmfit
On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote: Hi Doug, when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit. I don't understand what you mean. Can you elaborate? I am not sure why this is happening. In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those? Thanks, Caspar 2013/10/1 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote: Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? I just run a t-test of the r-values. I don't have a program to convert them to z-values, however, there are z-values that are created in the first level analysis. These are generated from the p-values but I bet it would give you the same thing. Use -m z with isxconcat-sess if you want to use the z. *Is the average r-value or z-value saved somewhere? Which level? For mri_glmfit, they are not, but it is not hard to get them with matlab. *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? Not usually, but it could be done by not including -no-whiten when you run mkanalysis-sess. I usually use the regression coefficients instead of correlation coefficients because that they are at least unbiased with respect to noise level and autocorrelation. doug I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center 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
Re: [Freesurfer] trouble with pial surface in v5.1
the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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] trouble with pial surface in v5.1
h. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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] Repost: pcc maps and mri_glmfit
Hi Doug, I loaded the pcc.nii file that I got from isxconcat-sess into Matlab and then ran a t-test against 0 over the 4th dimension. I converted the resulting p-values to -log10 and then compared them to the output of mri_glmfit, namely sig.vol. This was the mri_glmfit command: mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname I was expecting the p-values to be the same, which apparently is not the case, unless I am doing/understanding something wrong. By now, I am actually more inclined to use the regression coefficients instead. However, I'd still like to get pcc maps from them, if there is a way to do so in FSFAST. Thanks, Caspar 2013/10/3 Douglas N Greve gr...@nmr.mgh.harvard.edu On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote: Hi Doug, when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit. I don't understand what you mean. Can you elaborate? I am not sure why this is happening. In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those? Thanks, Caspar 2013/10/1 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote: Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? I just run a t-test of the r-values. I don't have a program to convert them to z-values, however, there are z-values that are created in the first level analysis. These are generated from the p-values but I bet it would give you the same thing. Use -m z with isxconcat-sess if you want to use the z. *Is the average r-value or z-value saved somewhere? Which level? For mri_glmfit, they are not, but it is not hard to get them with matlab. *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? Not usually, but it could be done by not including -no-whiten when you run mkanalysis-sess. I usually use the regression coefficients instead of correlation coefficients because that they are at least unbiased with respect to noise level and autocorrelation. doug I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_
Re: [Freesurfer] trouble with pial surface in v5.1
what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu h. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar 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] trouble with pial surface in v5.1
It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm. Caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu h. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing using the N3 tool but that didn't change anything. Thanks for any advice on this, Caspar The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] QDEC issues
Dear FreeSurfers, While running analyses in QDEC, it only allows me to select one continuous variable at a time instead of the usual two –so running analyses in QDEC is extremely limited. I have used QDEC before, and this is a new issue. Has anyone else encountered this problem? Thanks, Prapti - CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or legally privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of this original message. - ___ 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] aparcstats2table for manually drawn ROIs
Hi there, So I've run recon-all on my group of subjects, ran them in QDEC, manually drawn my ROIs, used mris_anatomical_stats to create a .stats files for each subject from my hand drawn ROIs and now I want to use aparcstats2table to gather the thicknesses from all my subjects Is there an option to gather stats from a particular .stats file rather than from just the two parcellation atlases? I think there is something similar in asegstats2table (--stats=lh.xxx.stats), but is there something like that for aparcstats2table? Many thanks, Jack ___ 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] aparcstats2table for manually drawn ROIs
Hi Jack,
You can specify the .stats file created. Here is an example from the script I
use.
Anyone, correct me if this is wrong!
Tara
mris_anatomical_stats -l ${subject}/label/lh.frontalmerge.label -f
${subject}/stats/lh_frontal_surface.stats ${subject} lh pial
aparcstats2table --hemi lh \
--subjects sub1 sub2 sub3 \
--meas thickness \
--parc lh_frontal_surface \
--tablefile lh.frontal_thickness.stats.txt
- Original Message -
From: Jackie Lam jackie@mail.mcgill.ca
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, October 3, 2013 12:51:21 PM
Subject: [Freesurfer] aparcstats2table for manually drawn ROIs
Hi there,
So I've run recon-all on my group of subjects, ran them in QDEC, manually drawn
my ROIs, used mris_anatomical_stats to create a .stats files for each subject
from my hand drawn ROIs and now I want to use aparcstats2table to gather the
thicknesses from all my subjects Is there an option to gather stats from a
particular .stats file rather than from just the two parcellation atlases? I
think there is something similar in asegstats2table (--stats=lh.xxx.stats), but
is there something like that for aparcstats2table?
Many thanks,
Jack
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Re: [Freesurfer] Repost: pcc maps and mri_glmfit
Hi Doug, On Thursday, October 3, 2013, Douglas N Greve wrote: It sounds like two issues: 1. p-values not consistent with your program. What did you use to compute? Did you do a two-sided (which is what fsfast uses)? I used ttest in Matlab, two sided. 2. Using pcc maps. Why not use -m pcc? Isn't that giving me a map per subject? How do I get the group map that is consistent with the results of mri_glmfit run on ces.nii? Thanks, Caspar doug On 10/03/2013 01:10 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I loaded the pcc.nii file that I got from isxconcat-sess into Matlab and then ran a t-test against 0 over the 4th dimension. I converted the resulting p-values to -log10 and then compared them to the output of mri_glmfit, namely sig.vol. This was the mri_glmfit command: mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname I was expecting the p-values to be the same, which apparently is not the case, unless I am doing/understanding something wrong. By now, I am actually more inclined to use the regression coefficients instead. However, I'd still like to get pcc maps from them, if there is a way to do so in FSFAST. Thanks, Caspar 2013/10/3 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.edu On 10/03/2013 10:39 AM, Caspar M. Schwiedrzik wrote: Hi Doug, when I run a two-tailed t-test against 0 in Matlab on the Rs in pcc.nii that I get out of isxconcat-sess with -m pcc, and DOF from ffxdof.dat, I get different -log10(p) values than the ones that come out of mri_glmfit. I don't understand what you mean. Can you elaborate? I am not sure why this is happening. In principle, I just want pcc maps as final output to show them on the surface (instead of p-values). So I'd be happy to follow your advice regarding the biasing effects of noise and autocorrelation and use the regression coefficients. However, mri_glmfit (v5.1) does not seem to output pcc maps of the contrasts (contrary to selxavg3-sess on the single subject level). How would I get those? Thanks, Caspar 2013/10/1 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu On 10/01/2013 01:13 PM, Caspar M. Schwiedrzik wrote: Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? I just run a t-test of the r-values. I don't have a program to convert them to z-values, however, there are z-values that are created in the first level analysis. These are generated from the p-values but I bet it would give you the same thing. Use -m z with isxconcat-sess if you want to use the z. *Is the average r-value or z-value saved somewhere? Which level? For mri_glmfit, they are not, but it is not hard to get them with matlab. *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? Not usually, but it could be done by not including -no-whiten when you run mkanalysis-sess. I usually use the regression coefficients instead of correlation coefficients because that they are at least unbiased with respect to noise level and autocorrelation. doug I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar __**_ Freesurfer mailing list
Re: [Freesurfer] aparcstats2table for manually drawn ROIs
Hi Tara,
Brilliant, that's exactly what I need. For some reason I was under the
impression that the --parc flag was restricted to either the Killiany/Desikan
atlas or the Destrieux atlas. Thanks again!
Jack
On 2013-10-03, at 2:03 PM, Tara Ann Miskovich misko...@uwm.edu
wrote:
Hi Jack,
You can specify the .stats file created. Here is an example from the script I
use.
Anyone, correct me if this is wrong!
Tara
mris_anatomical_stats -l ${subject}/label/lh.frontalmerge.label -f
${subject}/stats/lh_frontal_surface.stats ${subject} lh pial
aparcstats2table --hemi lh \
--subjects sub1 sub2 sub3 \
--meas thickness \
--parc lh_frontal_surface \
--tablefile lh.frontal_thickness.stats.txt
- Original Message -
From: Jackie Lam jackie@mail.mcgill.ca
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, October 3, 2013 12:51:21 PM
Subject: [Freesurfer] aparcstats2table for manually drawn ROIs
Hi there,
So I've run recon-all on my group of subjects, ran them in QDEC, manually
drawn my ROIs, used mris_anatomical_stats to create a .stats files for each
subject from my hand drawn ROIs and now I want to use aparcstats2table to
gather the thicknesses from all my subjects Is there an option to gather
stats from a particular .stats file rather than from just the two
parcellation atlases? I think there is something similar in asegstats2table
(--stats=lh.xxx.stats), but is there something like that for aparcstats2table?
Many thanks,
Jack
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Re: [Freesurfer] Why don't no-mask flag work?
preproc-sess -s SbjName -fwhm 2 -per-run -fsd bold -mni305-1mm -nomask -no-subcort-mask I also tried per-session and mni305-2mm but still did not help. I even tried doing it in native space (by not mentioning mni305/fsaverage) but did not work either. What was your preproc-sess command? On 10/03/2013 10:29 AM, SHAHIN NASR wrote: Hi Doug, Did you have a chance to find the reason for this problem? On Wed, Oct 2, 2013 at 3:20 PM, sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu wrote: I still receive the same error message (1mm is now 2mm in the message). outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask2 Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.2mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); Does the same thing happen if you use the 2mm instead of the 1mm? On 10/02/2013 02:21 PM, SHAHIN NASR wrote: Hi, I want to test activity outside the brain (around eyes/retina) but when I use -no-mask flag in my mkanalysis-sess (to be able to see activity outside brain) as below: mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force -runlistfile RunList -per-run -fsd bold -no-mask I get this error: outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.1mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); -- ERROR: fast_selxavg3() failed\n Note: ** I have already used -nomask and -no-subcort-mask in the preproc-sess *** If I remove this flag, everything looks fine except for the fact that all activity outside brain is masked! -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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.
Re: [Freesurfer] Why don't no-mask flag work?
OK, try it like this using the dev env 1. When you run preproc-sess use -no-subcort-mask but do not spec -nomask 2. When ruy run mkanalysis-sess use both -no-subcort-mask and -no-mask Note that the eyes may get cut off in the mni305 space. You might just want to keep it in native space. doug On 10/03/2013 03:19 PM, sha...@nmr.mgh.harvard.edu wrote: preproc-sess -s SbjName -fwhm 2 -per-run -fsd bold -mni305-1mm -nomask -no-subcort-mask I also tried per-session and mni305-2mm but still did not help. I even tried doing it in native space (by not mentioning mni305/fsaverage) but did not work either. What was your preproc-sess command? On 10/03/2013 10:29 AM, SHAHIN NASR wrote: Hi Doug, Did you have a chance to find the reason for this problem? On Wed, Oct 2, 2013 at 3:20 PM, sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu wrote: I still receive the same error message (1mm is now 2mm in the message). outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask2 Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.2mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); Does the same thing happen if you use the 2mm instead of the 1mm? On 10/02/2013 02:21 PM, SHAHIN NASR wrote: Hi, I want to test activity outside the brain (around eyes/retina) but when I use -no-mask flag in my mkanalysis-sess (to be able to see activity outside brain) as below: mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force -runlistfile RunList -per-run -fsd bold -no-mask I get this error: outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.1mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); -- ERROR: fast_selxavg3() failed\n Note: ** I have already used -nomask and -no-subcort-mask in the preproc-sess *** If I remove this flag, everything looks fine except for the fact that all activity outside brain is masked! -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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/ -- 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] bias field segmentation issue
Hello all, I'm trying to run Freesurfer recon-all on a series of T1 images with pretty extreme bias field intensity inhomogeneities. Signal dropoff in the inferior-most and superior-most slices results in temporal lobe and superior cortical volume underestimation. It's related to the coil and is stereotypically present in every one of the scans so there should be a way to correct them all for bulk processing. I tried N4 bias field correction which resulted in a modest improvement but was far from perfect. I also tried adding control points and rerunning a subset of 20 of them as suggested elsewhere in the forum. Adding the control points improved the subset slightly, but estimating bias field from those subjects and applying the correction to everyone else resulted in worse segmentation overall. Can anyone suggest a method for correcting this? Thanks in advance for any advice. -David ___ 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] Why don't no-mask flag work?
This time, selxavg3-sess finished without any error but everything outside the brain including eyes are cut (for me i.e. failure). Apparently, no-mask flag is ignored (!). To help you find the problem I copy/paste my commands here: preproc-sess -s Sbj_53/abir/ -fwhm 2 -per-session -fsd bold -no-subcort-mask mkanalysis-sess -analysis RetinaPrj_New -fwhm 2 -paradigm Conds.par -native -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -runlistfile RunList -per-session -fsd bold -no-subcort-mask -no-mask selxavg3-sess -s Sbj_53/abir -a RetinaPrj_New I am also attaching the analysis.info If you want to test the files, you can see the subject files in: /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir Note: I did all of these tests from scratch after deleting files from the previous tests. So it can't be due to a remaining file from the previous processes. On Thu, Oct 3, 2013 at 3:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: OK, try it like this using the dev env 1. When you run preproc-sess use -no-subcort-mask but do not spec -nomask 2. When ruy run mkanalysis-sess use both -no-subcort-mask and -no-mask Note that the eyes may get cut off in the mni305 space. You might just want to keep it in native space. doug On 10/03/2013 03:19 PM, sha...@nmr.mgh.harvard.edu wrote: preproc-sess -s SbjName -fwhm 2 -per-run -fsd bold -mni305-1mm -nomask -no-subcort-mask I also tried per-session and mni305-2mm but still did not help. I even tried doing it in native space (by not mentioning mni305/fsaverage) but did not work either. What was your preproc-sess command? On 10/03/2013 10:29 AM, SHAHIN NASR wrote: Hi Doug, Did you have a chance to find the reason for this problem? On Wed, Oct 2, 2013 at 3:20 PM, sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.**harvard.edu sha...@nmr.mgh.harvard.edu wrote: I still receive the same error message (1mm is now 2mm in the message). outanadir = /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/** Sbj_53/abir/bold/RetinaPrj_**nomask2 Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/** Sbj_53/abir/bold/008/masks/.**mni305.2mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); Does the same thing happen if you use the 2mm instead of the 1mm? On 10/02/2013 02:21 PM, SHAHIN NASR wrote: Hi, I want to test activity outside the brain (around eyes/retina) but when I use -no-mask flag in my mkanalysis-sess (to be able to see activity outside brain) as below: mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force -runlistfile RunList -per-run -fsd bold -no-mask I get this error: outanadir = /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/** Sbj_53/abir/bold/RetinaPrj_**nomask Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/**pitcairn/1/shahin/Retina_Prj/** Sbj_53/abir/bold/008/masks/.**mni305.1mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); --** ERROR: fast_selxavg3() failed\n Note: ** I have already used -nomask and -no-subcort-mask in the preproc-sess *** If I remove this flag, everything looks fine except for the fact that all activity outside brain is masked! -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
[Freesurfer] Patch x y z
Hello, read_patch (patch_name) gives x,y and z values. Are these vertex RAS? Thank you. Hiroyuki ___ 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] Patch x y z
yes, and all the z values should be zero if it has been flattened. Note that the coordinates in the flat space are pretty arbitrary cheers Bruce On Thu, 3 Oct 2013, Oya, Hiroyuki wrote: Hello, read_patch (patch_name) gives x,y and z values. Are these vertex RAS? Thank you. Hiroyuki ___ 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] Patch x y z
If I have vertices for making a new patch, is there any command line tool for this? Hiroyuki -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 October 2013 16:01 To: Oya, Hiroyuki Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Patch x y z yes, and all the z values should be zero if it has been flattened. Note that the coordinates in the flat space are pretty arbitrary cheers Bruce On Thu, 3 Oct 2013, Oya, Hiroyuki wrote: Hello, read_patch (patch_name) gives x,y and z values. Are these vertex RAS? Thank you. Hiroyuki Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ 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: Fwd: V1 label
Sure! Where/how do I upload the subject's folder? I've tried attaching a zipped copy to my email but it exceeds the size limit. Thanks! Krista On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Krista I've never seen that happen before. Can you upload this subject and we will take a look? thanks Bruce On Wed, 2 Oct 2013, krista kelly wrote: Hi Bruce, I've tried twice to post this to the freesurfer mail list but it hasn't worked, I'm assuming because of the attached pictures. I'm going to try this again with only one picture and see if it works. I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well. Here are the commands I ran: recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.**nii.gz By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left hemisphere with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer. Is there something I'm doing wrong? Please let me know you're not able to see the snapshots. Thanks! Krista On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Krista, which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce On Mon, 23 Sep 2013, krista kelly wrote: Hi all, I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below). Thanks! Hi Doug, Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below: recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.**nii.gz then recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.**nii.gz I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead? Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the process and I wouldn't want to mess with that too much. Thanks! On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: How did you do the transfer? What was your cmd line? doug On 09/10/2013 05:31 PM, krista kelly wrote: Hello, I am looking at cortical thickness and surface area using Freesurfer. I have transferred label V1 from freesurfer onto the brains of my participants and when I view them on the inflated brains in tksurfer , I notice that there are holes in the label. Is this an issue when calculating mean cortical thickness and total surface area estimations? Should I fill these in somehow? I've attached a picture to show as an example. Please let me know if the picture cannot be viewed. Thanks! Krista __**_ Freesurfer
Re: [Freesurfer] Fwd: Fwd: V1 label
you can do it here: https://gate.nmr.mgh.harvard.edu/filedrop2/ On Thu, 3 Oct 2013, krista kelly wrote: Sure! Where/how do I upload the subject's folder? I've tried attaching a zipped copy to my email but it exceeds the size limit. Thanks! Krista On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Krista I've never seen that happen before. Can you upload this subject and we will take a look? thanks Bruce On Wed, 2 Oct 2013, krista kelly wrote: Hi Bruce, I've tried twice to post this to the freesurfer mail list but it hasn't worked, I'm assuming because of the attached pictures. I'm going to try this again with only one picture and see if it works. I'm using the V1 labels that are automatically generated during recon-all (I think at autorecon step 28??). There are also V2 and MT labels that get generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and have tried in 5.1 as well. Here are the commands I ran: recon-all -all -notal-check -cw256 -force -subjid BV20 -i ~/Desktop/New_CT_niis/BV20.nii.gz By holes, I mean that when I look at the label on the 3d brain in tksurfer, there are areas on the surface that are coloured in by the label. I've attached a photograph of the left hemisphere with the V1 label overlaid. It's even worse, and in both hemispheres, when I look at the cuneus label automatically generated with freesurfer. Is there something I'm doing wrong? Please let me know you're not able to see the snapshots. Thanks! Krista On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Krista, which V1 label are you talking about? And when you say holes when you load it onto the 3D brain with tksurfer, what exactly do you mean? Can you send us a snapshot? Bruce On Mon, 23 Sep 2013, krista kelly wrote: Hi all, I'm having trouble with V1 labels that are mapped automatically in freesurfer. I've noticed that there are holes in the label when I load it onto a 3d brain in tksurfer. This happens more often for the left hemisphere and not so much for the right. I've found the problem persists even after doing manual edits of the borders and fixing the brain extraction. I was just wondering if anyone has had the same problem or knows how to fix it (see message previously posted below). Thanks! Hi Doug, Sorry it's been a while since I've ran the initial codes, but I think these are the labels automatically generated by Freesurfer v5.0 during recon-all (correct me if I'm wrong). Here's what I ran below: recon-all -all -notal-check -cw256 -force -subjid MB18 -i ~/Desktop/New_CT_niis/MB18.nii.gz then recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz I've checked a few more brains and noticed the same problem. I've also noticed that the left hemisphere is always worse than the right. When opening the brains in tkmedit, the labels are not continuous on the surface. Could this be the problem? Is this label the same as the Hinds label and if not, should I run that instead? Is possible to edit the label, and if so, how often does one have to edit the labels automatically created by freesurfer? I know that too much editing can take away from the standardization of the
Re: [Freesurfer] trouble with pial surface in v5.1
Hi Bruce, sorry, I meant to say that data is conformed. It is primate data. I am having trouble with this particular data set only; the other ones are at the same resolution and worked fine. I am attaching another screenshot to show that the control points unfortunately do not solve the problem. See occipital lobe. Caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar, that's probably part of the problem. Is this human data? If you actually run it at 1mm (conforming it) does it work better? Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: It is originally 0.5x0.5x0.5 mm but we are pretending it's 1x1x1 mm. Caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu what resolution? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: This was a fairly regular MPRAGE, unfortunately not very well optimized for contrast. However, the main issue seems to be that the data were acquired with a surface coil here. That made some of the brain extremely bright (close to the coil) and some of the brain pretty dark (far away from the coil). In the screenshot that I sent you, there is some gray matter that has values between 95-100, which is well captured by the pial surface, while the grey matter in the more medial areas has values between 70 and 80. The transition where the pial surface starts to fail is when the gray matter values drop from above 90 to below 90. Caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu h. Can you tell us more about the acquisition? On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: the white matter is mostly between 100 and 110 in these regions. at least in the center of the wm, the voxels are almost all 110. caspar 2013/10/3 Bruce Fischl fis...@nmr.mgh.harvard.edu is the WM in those regions already close to 110? No, there is no way to normalize GM intensity (it has too much biological variability over the brain) On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Thanks, Bruce. The problem is fairly extensive. There is no way to do normalize grey matter intensity (the white surface looks pretty good)?Caspar On Thursday, October 3, 2013, Bruce Fischl wrote: Hi Caspar try putting control points in the white matter where the pial surface doesn't get out far enough. cheers Bruce On Thu, 3 Oct 2013, Caspar M. Schwiedrzik wrote: Hi Freesurfer Experts, I am working on a fairly noisy and inhomogeneous MPRAGE T1 and I am having trouble getting the pial surface to go all the way through the grey matter. Please see screenshot attached. These data were acquired with a surface coil and the grey matter varies a lot in intensity. Interestingly, the pial surface growing process fails where the grey matter is fairly dark. I have tried several rounds of normalizing
[Freesurfer] FSL masks applied to Freesurfer surfaces?
Hi, I'd like to take some masks that I have in MNI standard space in FSL and map them to Freesurfer surface space. The goal is to extract measures of average cortical thickness (or area or etc) for those regions for each subject. Is there a standard way to do this? ___ 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.
