[Freesurfer] re error when making average subject
Hi all, I was trying to create an average subject however received this error message. I temporarily removed that subject however I was wondering what a possible cause for this error is? Applying LTAtransformInterp (resample_type 1) writing to /sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/avgsubject/tmp/make_average_vol-tmp-10132/T1-EHRS_0764_1.mgh... mri_convert /sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/EHRS_0774_1/mri/T1.mgz /sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/avgsubject/tmp/make_average_vol-tmp-10132/T1-EHRS_0774_1.mgh --apply_transform /sdata/images/projects/EHRS/2/Freesurfer_EHRS/READYFORANALYSIS/EHRS_0774_1/mri/transforms/talairach.xfm -oc 0 0 Segmentation fault /home/orkney_01/cbois ERROR: mri_convert failed. ERROR: make_average_volume [cbois@poplar ~]$ Thank you very much for your help Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] creating 'Mid' surfaces
Dear FreeSurfer Experts, What is the best way of creating surfaces approximating layer IV of the cortex or the 'mid' surface (I.e. Surface between grey and white matter). Thank you very much for your help. Regards, Christine ___ 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] ROI analysis and whitening in fsfast - Percent activity change
Hi Doug and the list,
I think I still have a problem understanding what cesvar.nii contains. As a
sanity check, I tried to create 95% confidence intervals around my CES. I found
that in some voxels (or ROIs in my case) that had a p-value of less than 0.05,
my 95% confidence interval for my CES included zero. Here's one example:
clear
cesNii = MRIread('ces.nii');
cesVol = cesNii.vol;
cesVarNii = MRIread('cesvar.nii');
cesVarVol = cesVarNii.vol;
sigNii = MRIread('sig.nii');
sigVol = sigNii.vol;
pValue = 10^-abs(sigVol(4,1,1))
pValue =
0.0199
ces = cesVol(4,1,1)
ces =
-0.0028
cesVar = cesVarVol(4,1,1)
cesVar =
6.4511e-06
ces95pctCI = ces + [ -1 +1 ] .* sqrt(cesVar) * 1.96
ces95pctCI =
-0.00780.0022
Are the p-values calculated in a way that assumes non-Gaussian error of the
ces, or am I otherwise doing something wrong?
Thanks,
Clark
Douglas N
Grevehttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Douglas+N+Greve%22
Wed, 13 Feb 2013 15:11:27
-0800http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20130213
1). Yes
2) Right, pull the scale outside of the sqrt()
doug
On 02/13/2013 03:36 PM, Clark Fisher wrote:
Hi Doug,
Thanks for the help, that seemed to worked great. I have a few
follow up questions about how to process the resulting statistics.
I'm still using v4.5 (can't switch to v5 yet), as I mentioned, and
would like to get the % signal change for certain contrasts with error
bars. Looking through the listserv, I see that the values in
cespct.nii require correction by a scale factor in this version of
fsfast. The most recent conversation I could find on this comes from
2010, when you told Thomas Janssens:
Hi Thomas, you may have found a bug in my scale factor calculation. Can
you compute the new scale factor as described below? BTW, these issues
are fixed in version 5.
cd bold/analysis
x = load('X');
tirf = x.flac0.ev(3).tirf;
Xirf = x.flac0.ev(3).Xirf;
scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)]));
TR = x.flac0.TR;
dt = tirf(2)-tirf(1);
scalefNew = sum(Xirf)*TR/dt;
I can't find a follow up to this message. 2 questions.
1) The results with scalefNew look reasonable to me; do you still think that
this is the proper way to adjust cespct.nii in v4.5?
2) If I want to put error bars on my % signal change, how do I scale the
values in cesvarpct.nii? I would guess that if I wanted to put a 95% CI on
my % signal change, it would be:
(cespct * scalefNew) +/- ( sqrt(cesvarpct) * scalefNew * 1.96) and NOT
(cespct * scalefNew) +/- ( sqrt(cesvarpct * scalefNew) * 1.96)
Does this sound right, or am I misinterpreting what cesvarpct.nii contains?
Thanks again,
Clark
Hi Clark,
On 02/06/2013 05:55 PM, Clark Fisher wrote:
Hi everyone,
In a previous discussion on this list
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html),
Pablo Polosecki was asking the best way to perform hypothesis testing
using functional data within an ROI. The final opinion was that it
was best to average all of the time courses in the ROI, and re-run the
analysis from scratch, so that all of the appropriate whitening, etc.
occurred.
I was considering doing this, creating a small volume (say, 10 voxels
total) that had each voxel holding the average time course from one of
10 ROIs. I would then set up and run a usual fsfast analysis using
these tiny volumes. I am using freesurfer 4.5. I have a few questions.
1) Is this reasonable?
In general, it is reasonable. Though I'm curious what you are ultimately
trying to do. Do you want p-values for each subject in each ROI? Or will
you be combining the ROI beta values across subject in a group analysis?
If so, then the whitening will probably make little, if any, difference,
especially if this is a blocked design. In expectation, the whitening
does not affect the beta values.
2) One area where I expect to run into problems is with the whitening.
If I set -acfbins to the total number of my dummy voxels, and
-acffwhm to 0, will this use the autocorrelation function of the
average timecourse within each individual ROI? Is that an appropriate
approach? How sensitive will this be to the number of actual voxels
averaged to get each ROI (for instance, would this bias me to finding
more significant results in ROIs containing fewer voxels?).
That might work, but no promises! It is an appropriate approach. It
might be sensitive to the number of voxels if the number is small (say,
less than 100).
3) Are there other steps that depend upon the spatial arrangement of
voxels that I am forgetting, and will these steps choke on these small
volumes (or worse, fail in silent but pernicious ways).
Nothing I can think of off the top of my head.
doug
Thanks for all of the help,
Clark
___
Freesurfer mailing list
Re: [Freesurfer] creating 'Mid' surfaces
Hi Christine we use mris_expand for this. E.g. from the surf dir mris_expand -thickness lh.white 0.5 lh.mid cheers Bruce On Thu, 14 Feb 2013, Ecker, Christine wrote: Dear FreeSurfer Experts, What is the best way of creating surfaces approximating layer IV of the cortex or the 'mid' surface (I.e. Surface between grey and white matter). Thank you very much for your help. Regards, Christine ___ 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] creating 'Mid' surfaces
Hi Christine, If you cd to the subject directory you can locate the ?h.white surface and use mris_expand command to do this. Hth, Shantanu On Thu, February 14, 2013 5:39 am, Ecker, Christine wrote: Dear FreeSurfer Experts, What is the best way of creating surfaces approximating layer IV of the cortex or the 'mid' surface (I.e. Surface between grey and white matter). Thank you very much for your help. Regards, Christine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] creating 'Mid' surfaces
sorry the files are in the surf directory On Thu, February 14, 2013 9:53 am, Shantanu Ghosh wrote: Hi Christine, If you cd to the subject directory you can locate the ?h.white surface and use mris_expand command to do this. Hth, Shantanu On Thu, February 14, 2013 5:39 am, Ecker, Christine wrote: Dear FreeSurfer Experts, What is the best way of creating surfaces approximating layer IV of the cortex or the 'mid' surface (I.e. Surface between grey and white matter). Thank you very much for your help. Regards, Christine ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] nu_estimate_np_and_em error during recon-all
Tudor, Now that there is free space on the virtualbox ubuntu disk, are you able to complete recon-all's on data that is located on your external disk? I ask because although i'm not certain, i think nu_correct uses tmp space on the ubuntu local drive, which if it was full would cause recon failure on external data. Thats my theory anyway. We no longer have our local VirtualBox expert that created this to support this issue, so this might take some struggle. Nick Thanks Nick, it seems disk space is the issue after all, as /dev/sda1 has 0KB available space, due to the way the FS/Virtualbox drive was created (i.e. size-tailored to the FS installation). My files were in the folder that I shared through Virtualbox though (/media/Dell), which has plenty of space available, and that's where I ran recon-all from! Shouldn't I have 2GB of space in *that* folder? If not, then the issue of making space available in the home drive (or whatver it's called), i.e. in /dev/sda1, is, as it seems, a very non-trivial issue, which I have unsuccessfully tried to seek help with on the Virtualbox forum. Output of df -h below. *FreeSurfer:~ df -h FilesystemSize Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell* On 13 February 2013 20:47, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, I dont have any other suggestions, other than to make sure, as i mentioned before, then you have free space on the disk that appears within Xubuntu. That is, from a terminal, when you type: df -h you should see that /dev/sda1 has about 2GB of space. the nu_correct tools will fail if there is not enough disk space. Nick On Wed, 2013-02-13 at 18:32 +, Tudor Popescu wrote: Hi Nick, I was wondering if there might be any other solutions left for me to try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the baseline (bert) command past that nu_correct error. In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain the exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's VMWare to use on the 64-bit OS, as you suggested, however their website is down at the moment. Many thanks for your help. Tudor On 6 February 2013 16:12, Tudor Popescu tud...@gmail.com wrote: Hi Nick, Unfortunately I don't think I can run that version, as my OS (Win XP) is 32 bit. Is there nothing else I can try? Searching the list for error messages related to those nu_ components, it seems that many people have had this problem before. Were most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor On 6 February 2013 16:06, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution. Nick On Wed, 2013-02-06 at 12:59 +, Tudor Popescu wrote: ..I also did the following in the meantime, to make sure that the problem isn't due to a path error: - ran nu_estimate_np_and_em and nu_correct: both seem to respond fine, and they return their version number - checked env variables $MNI_PERL5LIB and $MNI_DATAPATH: both point into $FREESURFER_HOME/mni , as they should Still cannot get recon-all to run because of the error mentioned previously currently at my wit's end! :( On 4 February 2013 10:29, Tudor Popescu tud...@gmail.com wrote: Hi NIck, I too thought disk space might be an issue, however I''ve been
Re: [Freesurfer] longitudinal processing of one timepoint
Hi Luigi, 1 is the right way of calling it. 2 will have a negative effect in the sense that it takes the same image twice and then creates the mid-space at the same location, so 2 could be biased. 1 is creating an artifical mid-space and makes sure the image gets mapped there. Best, Martin On 02/13/2013 08:39 AM, Luigi Angelo Maglanoc wrote: Dear FreeSurfer experts, I know that it is possible to submit data with only one timepoint into the longitudinal stream with FreeSurfer 5.2. My question is, what is the exact command? is it: 1) recon-all -base templateid -tp tp1id -all or 2) recon-all -base templateid -tp tp1id -tp tp1id -all I have accidently run them with the second command, and I am also wondering whether this will have a negative impact? Thank you for your time and consideration! Sincerely Luigi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter 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] CORRECTING DEFECT
Dear All, I have been trying to recon all a patient and unfortunately nothing is happening after 24 hrs of processing so far .No error messages are coming up either .This is the line it got stuck,CORRECTING DEFECT 10 vertices 67735 convex hull 9509 This is a rerun after my initial processing failed for the same data set ,and patiently waited 36 hrs at Correcting Defect 10 before logging off .Do you know why this is happening.Does it have some thing to do with the data itself. In Thanks Chikku ___ 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] CORRECTING DEFECT
Hi Chikku, look at the wm.mgz to see if the cerebellum is still attached doug On 02/14/2013 11:22 AM, Varghese Chikku wrote: Dear All, I have been trying to recon all a patient and unfortunately nothing is happening after 24 hrs of processing so far .No error messages are coming up either .This is the line it got stuck,CORRECTING DEFECT 10 vertices 67735 convex hull 9509 This is a rerun after my initial processing failed for the same data set ,and patiently waited 36 hrs at Correcting Defect 10 before logging off .Do you know why this is happening.Does it have some thing to do with the data itself. In Thanks Chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ROI analysis and whitening in fsfast - Percent activity change
You can compute the t = ces/sqrt(cesvar) and from that (and the DOF) you
can compute the p to see if it is consistent with pValue.
doug
ps. I don't know that your conf interval formula is correct. I don't
have a reason to think it is wrong, I just don't know, so you might want
to double check it
On 02/14/2013 07:25 AM, Clark Fisher wrote:
Hi Doug and the list,
I think I still have a problem understanding what cesvar.nii contains.
As a sanity check, I tried to create 95% confidence intervals around
my CES. I found that in some voxels (or ROIs in my case) that had a
p-value of less than 0.05, my 95% confidence interval for my CES
included zero. Here's one example:
clear
cesNii = MRIread('ces.nii');
cesVol = cesNii.vol;
cesVarNii = MRIread('cesvar.nii');
cesVarVol = cesVarNii.vol;
sigNii = MRIread('sig.nii');
sigVol = sigNii.vol;
pValue = 10^-abs(sigVol(4,1,1))
pValue =
0.0199
ces = cesVol(4,1,1)
ces =
-0.0028
cesVar = cesVarVol(4,1,1)
cesVar =
6.4511e-06
ces95pctCI = ces + [ -1 +1 ] .* sqrt(cesVar) * 1.96
ces95pctCI =
-0.00780.0022
Are the p-values calculated in a way that assumes non-Gaussian error
of the ces, or am I otherwise doing something wrong?
Thanks,
Clark
Douglas N Greve
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Douglas+N+Greve%22
Wed, 13 Feb 2013 15:11:27 -0800
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20130213
1). Yes
2) Right, pull the scale outside of the sqrt()
doug
On 02/13/2013 03:36 PM, Clark Fisher wrote:
Hi Doug,
Thanks for the help, that seemed to worked great. I have a few
follow up questions about how to process the resulting statistics.
I'm still using v4.5 (can't switch to v5 yet), as I mentioned, and
would like to get the % signal change for certain contrasts with error
bars. Looking through the listserv, I see that the values in
cespct.nii require correction by a scale factor in this version of
fsfast. The most recent conversation I could find on this comes from
2010, when you told Thomas Janssens:
Hi Thomas, you may have found a bug in my scale factor calculation. Can
you compute the new scale factor as described below? BTW, these issues
are fixed in version 5.
cd bold/analysis
x = load('X');
tirf = x.flac0.ev(3).tirf;
Xirf = x.flac0.ev(3).Xirf;
scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)]));
TR = x.flac0.TR;
dt = tirf(2)-tirf(1);
scalefNew = sum(Xirf)*TR/dt;
I can't find a follow up to this message. 2 questions.
1) The results with scalefNew look reasonable to me; do you still think
that
this is the proper way to adjust cespct.nii in v4.5?
2) If I want to put error bars on my % signal change, how do I scale the
values in cesvarpct.nii? I would guess that if I wanted to put a 95% CI on
my % signal change, it would be:
(cespct * scalefNew) +/- ( sqrt(cesvarpct) * scalefNew * 1.96) and
NOT
(cespct * scalefNew) +/- ( sqrt(cesvarpct * scalefNew) * 1.96)
Does this sound right, or am I misinterpreting what cesvarpct.nii contains?
Thanks again,
Clark
Hi Clark,
On 02/06/2013 05:55 PM, Clark Fisher wrote:
Hi everyone,
In a previous discussion on this list
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html),
Pablo Polosecki was asking the best way to perform hypothesis testing
using functional data within an ROI. The final opinion was that it
was best to average all of the time courses in the ROI, and re-run the
analysis from scratch, so that all of the appropriate whitening, etc.
occurred.
I was considering doing this, creating a small volume (say, 10 voxels
total) that had each voxel holding the average time course from one of
10 ROIs. I would then set up and run a usual fsfast analysis using
these tiny volumes. I am using freesurfer 4.5. I have a few questions.
1) Is this reasonable?
In general, it is reasonable. Though I'm curious what you are ultimately
trying to do. Do you want p-values for each subject in each ROI? Or will
you be combining the ROI beta values across subject in a group analysis?
If so, then the whitening will probably make little, if any, difference,
especially if this is a blocked design. In expectation, the whitening
does not affect the beta values.
2) One area where I expect to run into problems is with the whitening.
If I set -acfbins to the total number of my dummy voxels, and
-acffwhm to 0, will this use the autocorrelation function of the
average timecourse within each individual ROI? Is that an appropriate
approach? How sensitive will this be to the number of actual voxels
averaged to get each ROI (for instance, would this bias me to finding
more significant results in ROIs containing fewer voxels?).
That might work, but no promises! It is an appropriate approach. It
might be
[Freesurfer] talairach transformation troubleshooting problem
Dear All, When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside the green line. Instead of drawing the green line to include all of the white matter of the whole brain, it somehow only includes the bottom half of the white matter of the brain. Is there a way to fix that? Thanks, Catherine___ 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] running freesurfer on multi core machine
Hi, I am runnning fressurfer on a Mac with 23.06 Ghz 6-core intel Xeon processors. is it possible to run recon-all and trac-all on multiple cores. Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] CORRECTING DEFECT
or if the skull is attached or the two hemis. The time it takes to correct a defect is quadratic in the size of the (convex hull of) the defect, so small ones are fast, and big ones take forever. Anything over 15K vertices or so usually means there is something dramatically wrong with your data. You can look at the ?h.orig.nofix or ?h.inflated.nofix surfaces to get an idea cheers Bruce On Thu, 14 Feb 2013, Douglas N Greve wrote: Hi Chikku, look at the wm.mgz to see if the cerebellum is still attached doug On 02/14/2013 11:22 AM, Varghese Chikku wrote: Dear All, I have been trying to recon all a patient and unfortunately nothing is happening after 24 hrs of processing so far .No error messages are coming up either .This is the line it got stuck,CORRECTING DEFECT 10 vertices 67735 convex hull 9509 This is a rerun after my initial processing failed for the same data set ,and patiently waited 36 hrs at Correcting Defect 10 before logging off .Do you know why this is happening.Does it have some thing to do with the data itself. In Thanks Chikku ___ 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] running freesurfer on multi core machine
yes, some of our binaries will make use of multiple cores, starting with version 5.2. You need to specify how many to use on the recon-all command line with -openmp N On Thu, 14 Feb 2013, Jon Wieser wrote: Hi, I am runnning fressurfer on a Mac with 23.06 Ghz 6-core intel Xeon processors. is it possible to run recon-all and trac-all on multiple cores. Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] talairach transformation troubleshooting problem
Hi Catherine can you send us an image of what you are looking at? thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote: Dear All, When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside the green line. Instead of drawing the green line to include all of the white matter of the whole brain, it somehow only includes the bottom half of the white matter of the brain. Is there a way to fix that? Thanks, Catherine ___ 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] nu_estimate_np_and_em error during recon-all
Tudor, In the default installation, there should be 2GB of free space on the default disk, so somehow it got filled. Try deleting unnecessary stuff (packages added during an upgrade I think mentioned doing, or subjects in the freesurfer/subjects dir). Freeing just a few tens of MB should be enough to get things working again. Nick Hi Nick, I don't think there *is* any free space on the virtualbox ubuntu disk - that disk would presumably correspond to the first row in the df -h output, which shows as 0 free space. So even for recon-alls ran on data located on external HDDs, I would expect the nu_correct error to come up on all FS/VirtualBox installations, assuming that tmp space is a requirement (which makes sense). However, you mentioned at some point that bert runs to completion in the fsv5.1 WindowsVM for other users, which is intriguing... Tudor On 14 February 2013 15:29, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, Now that there is free space on the virtualbox ubuntu disk, are you able to complete recon-all's on data that is located on your external disk? I ask because although i'm not certain, i think nu_correct uses tmp space on the ubuntu local drive, which if it was full would cause recon failure on external data. Thats my theory anyway. We no longer have our local VirtualBox expert that created this to support this issue, so this might take some struggle. Nick Thanks Nick, it seems disk space is the issue after all, as /dev/sda1 has 0KB available space, due to the way the FS/Virtualbox drive was created (i.e. size-tailored to the FS installation). My files were in the folder that I shared through Virtualbox though (/media/Dell), which has plenty of space available, and that's where I ran recon-all from! Shouldn't I have 2GB of space in *that* folder? If not, then the issue of making space available in the home drive (or whatver it's called), i.e. in /dev/sda1, is, as it seems, a very non-trivial issue, which I have unsuccessfully tried to seek help with on the Virtualbox forum. Output of df -h below. *FreeSurfer:~ df -h FilesystemSize Used Avail Use% Mounted on /dev/sda1 11G 9.8G 0 100% / tmpfs 755M 0 755M 0% /lib/init/rw varrun755M 104K 754M 1% /var/run varlock 755M 0 755M 0% /var/lock udev 755M 152K 754M 1% /dev tmpfs 755M 0 755M 0% /dev/shm lrm 755M 2.4M 752M 1% /lib/modules/2.6.28-11-generic/volatile overflow 1.0M 12K 1012K 2% /tmp Dell 173G 106G 68G 62% /media/Dell* On 13 February 2013 20:47, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, I dont have any other suggestions, other than to make sure, as i mentioned before, then you have free space on the disk that appears within Xubuntu. That is, from a terminal, when you type: df -h you should see that /dev/sda1 has about 2GB of space. the nu_correct tools will fail if there is not enough disk space. Nick On Wed, 2013-02-13 at 18:32 +, Tudor Popescu wrote: Hi Nick, I was wondering if there might be any other solutions left for me to try, as I am currently stuck in the first (recon-all) stage of my cortical thickness analysis, not even being able to get the baseline (bert) command past that nu_correct error. In the meantime I installed FreeSurfer on a different computer, running WinXP 64-bit, and tried the command there, only to obtain the exact same error, even though the total amount of memory there was over 3GB, and disk space was plenty. I tried downloading FSL's VMWare to use on the 64-bit OS, as you suggested, however their website is down at the moment. Many thanks for your help. Tudor On 6 February 2013 16:12, Tudor Popescu tud...@gmail.com wrote: Hi Nick, Unfortunately I don't think I can run that version, as my OS (Win XP) is 32 bit. Is there nothing else I can try? Searching the list for error messages related to those nu_ components, it seems that many people have had this problem before. Were most of these cases related to N3/MNI? In my case, this doesn't seem to be the cause of the error. Tudor On 6 February 2013 16:06, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution.
Re: [Freesurfer] talairach transformation troubleshooting problem
probably not, although it's hard to say. If you upload the whole subject dir I'll take a look. How does the aseg look? On Thu, 14 Feb 2013, Rongxiang Tang wrote: Hi Bruce, I checked the skullstrip stage using this command: tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs and both of the brainmask and T1 images look fine the wm.mgz is problema tic, with some area missing. I was wondering if I need to manually adding control points to solve the pro blem. Thanks, Catherine From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Rongxiang Tang rongxiangt...@yahoo.com Sent: Thursday, February 14, 2013 2:03 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem Hi Catherine that looks like something went wrong in the surface recon, not in the talairaching. Maybe a skullstrip problem? You need to investigate. Also, please cc the list so that others can answer! thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote: Hi Bruce, I attached two images...one is the target view and the other is the moveable view. Thanks, Catherine ___ _ From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Rongxiang Tang rongxiangt...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 14, 2013 1:33 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem Hi Catherine can you send us an image of what you are looking at? thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote: Dear All, When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside the green line. Instead of drawing the green line to include all of the white matter of the whole brain, it somehow only includes the bottom half of the white matter of the brain. Is there a way to fix that? Thanks, Catherine 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] talairach transformation troubleshooting problem
Hi Bruce, The aseg is also problematic for several slicesI uploaded the subject dir on theMatinos center file drop...since the file is too big, I separated into two parts. Thanks, Catherine From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Rongxiang Tang rongxiangt...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 14, 2013 2:42 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem probably not, although it's hard to say. If you upload the whole subject dir I'll take a look. How does the aseg look? On Thu, 14 Feb 2013, Rongxiang Tang wrote: Hi Bruce, I checked the skullstrip stage using this command: tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs and both of the brainmask and T1 images look fine the wm.mgz is problema tic, with some area missing. I was wondering if I need to manually adding control points to solve the pro blem. Thanks, Catherine From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Rongxiang Tang rongxiangt...@yahoo.com Sent: Thursday, February 14, 2013 2:03 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem Hi Catherine that looks like something went wrong in the surface recon, not in the talairaching. Maybe a skullstrip problem? You need to investigate. Also, please cc the list so that others can answer! thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote: Hi Bruce, I attached two images...one is the target view and the other is the moveable view. Thanks, Catherine ___ _ From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Rongxiang Tang rongxiangt...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 14, 2013 1:33 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem Hi Catherine can you send us an image of what you are looking at? thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote: Dear All, When I was checking the talairach transformation output, I noticed that some of the white matter was not included inside the green line. Instead of drawing the green line to include all of the white matter of the whole brain, it somehow only includes the bottom half of the white matter of the brain. Is there a way to fix that? Thanks, Catherine 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] ROI analysis and whitening in fsfast - Percent activity change
Thanks - it turned out that the zero voxels I put in my fake ROI volumes were
causing the cesvar voxels to be misaligned relative to the ces voxels. All
seems to be right for the moment.
-Clark
On Feb 14, 2013, at 12:47 PM, Douglas N Greve wrote:
You can compute the t = ces/sqrt(cesvar) and from that (and the DOF) you can
compute the p to see if it is consistent with pValue.
doug
ps. I don't know that your conf interval formula is correct. I don't have a
reason to think it is wrong, I just don't know, so you might want to double
check it
On 02/14/2013 07:25 AM, Clark Fisher wrote:
Hi Doug and the list,
I think I still have a problem understanding what cesvar.nii contains. As a
sanity check, I tried to create 95% confidence intervals around my CES. I
found that in some voxels (or ROIs in my case) that had a p-value of less
than 0.05, my 95% confidence interval for my CES included zero. Here's one
example:
clear
cesNii = MRIread('ces.nii');
cesVol = cesNii.vol;
cesVarNii = MRIread('cesvar.nii');
cesVarVol = cesVarNii.vol;
sigNii = MRIread('sig.nii');
sigVol = sigNii.vol;
pValue = 10^-abs(sigVol(4,1,1))
pValue =
0.0199
ces = cesVol(4,1,1)
ces =
-0.0028
cesVar = cesVarVol(4,1,1)
cesVar =
6.4511e-06
ces95pctCI = ces + [ -1 +1 ] .* sqrt(cesVar) * 1.96
ces95pctCI =
-0.00780.0022
Are the p-values calculated in a way that assumes non-Gaussian error of the
ces, or am I otherwise doing something wrong?
Thanks,
Clark
Douglas N Greve
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from:%22Douglas+N+Greve%22
Wed, 13 Feb 2013 15:11:27 -0800
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=date:20130213
1). Yes
2) Right, pull the scale outside of the sqrt()
doug
On 02/13/2013 03:36 PM, Clark Fisher wrote:
Hi Doug,
Thanks for the help, that seemed to worked great. I have a few
follow up questions about how to process the resulting statistics.
I'm still using v4.5 (can't switch to v5 yet), as I mentioned, and
would like to get the % signal change for certain contrasts with error
bars. Looking through the listserv, I see that the values in
cespct.nii require correction by a scale factor in this version of
fsfast. The most recent conversation I could find on this comes from
2010, when you told Thomas Janssens:
Hi Thomas, you may have found a bug in my scale factor calculation. Can
you compute the new scale factor as described below? BTW, these issues
are fixed in version 5.
cd bold/analysis
x = load('X');
tirf = x.flac0.ev(3).tirf;
Xirf = x.flac0.ev(3).Xirf;
scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)]));
TR = x.flac0.TR;
dt = tirf(2)-tirf(1);
scalefNew = sum(Xirf)*TR/dt;
I can't find a follow up to this message. 2 questions.
1) The results with scalefNew look reasonable to me; do you still think
that
this is the proper way to adjust cespct.nii in v4.5?
2) If I want to put error bars on my % signal change, how do I scale the
values in cesvarpct.nii? I would guess that if I wanted to put a 95% CI
on
my % signal change, it would be:
(cespct * scalefNew) +/- ( sqrt(cesvarpct) * scalefNew * 1.96) and
NOT
(cespct * scalefNew) +/- ( sqrt(cesvarpct * scalefNew) * 1.96)
Does this sound right, or am I misinterpreting what cesvarpct.nii
contains?
Thanks again,
Clark
Hi Clark,
On 02/06/2013 05:55 PM, Clark Fisher wrote:
Hi everyone,
In a previous discussion on this list
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html),
Pablo Polosecki was asking the best way to perform hypothesis testing
using functional data within an ROI. The final opinion was that it
was best to average all of the time courses in the ROI, and re-run the
analysis from scratch, so that all of the appropriate whitening, etc.
occurred.
I was considering doing this, creating a small volume (say, 10 voxels
total) that had each voxel holding the average time course from one of
10 ROIs. I would then set up and run a usual fsfast analysis using
these tiny volumes. I am using freesurfer 4.5. I have a few
questions.
1) Is this reasonable?
In general, it is reasonable. Though I'm curious what you are ultimately
trying to do. Do you want p-values for each subject in each ROI? Or will
you be combining the ROI beta values across subject in a group analysis?
If so, then the whitening will probably make little, if any, difference,
especially if this is a blocked design. In expectation, the whitening
does not affect the beta values.
2) One area where I expect to run into problems is with the whitening.
If I set -acfbins to the total number of my dummy voxels, and
-acffwhm to 0, will this use the autocorrelation function of the
average timecourse within each individual ROI? Is that an
