[Freesurfer] Longitudinal - varying geometries
Dear FreeSurfers, I have read in the Mailing list (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html and others) other users asking questioning in regard of a Warning from FreeSurfer 5.3 longitudinal pipeline (-base step): \n*** WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ***\n I am working in a sample with a longotudinal design which receives this warn, although there was no change in hardware, and (supposedly) the acquisition protocol was the same. As requested by Martin in former posts in the Mailing List, I attached the output from mri_info */rawavg.mgz. I would like to know if these differences should be considered a bias in a longitudinal study and, if they should, if there is a way to fix it. Regards, Pedro Rosa. baseline Description: Binary data fup Description: Binary data ___ 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] Fw: longitudinal statistics LGI
Hi Jorge,
Which direction does this contrast show? con pat is redis or vice versa?
I mean how can one interpret the result?
Best regards,
Amirhossein Manzouri
On Sat, Mar 28, 2015 at 3:46 PM, jorge luis jbernal0...@yahoo.es wrote:
Hi Amirhossein
You need another column in your design matrix to encode the group. That
new column is 0 for control's row and 1 for patient's rows. the contrast to
test for population group differences is then [0 0 1].
-Jorge
--
*De:* amirhossein manzouri a.h.manzo...@gmail.com
*Para:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu
*CC:* jorge luis jbernal0...@yahoo.es
*Enviado:* Jueves 26 de marzo de 2015 10:50
*Asunto:* Re: [Freesurfer] Fw: longitudinal statistics LGI
Hi Jorge,
I have read the previous posts and applied it for my analysis which is
longitudinal study go control and patient groups. I have a control group
(n=19) with 2.87 ± 0.3 years time difference between scans. and patient
group (n=16) who have 1.31 ± 0.6 years time difference. I followed your
instructions first in each group separately , for example in control group
I have read the data:
1-Read your label eg.:
*lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label'); *
2-Read the data file eg.:
*[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');*
Then X which is 38x2 double , first column is all ones and second is 0 and
time difference every one row for each subject , so I want to see thickness
change so I used :
3-Fit a vertex-wise lme model with two random effects for the intercept
term and time eg.:
*lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);*
Having first column as all ones and second the time difference , I made
the contrast to look at thickness changes within group:
*CM.C = [1 0];*
4-Perform vertex-wise inferences eg.:
*F_lhstats = lme_mass_F(lhstats1, CM);*
5-Save results eg.:
*fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig'); *
*Would you please let me know if the approach is correct ? and if I want
to add the patient group should I do the same just change the contrast ?*
*Best regards,*
Best regards,
Amirhossein Manzouri
On Fri, Mar 13, 2015 at 5:52 PM, Jon Alan Wieser wie...@uwm.edu wrote:
--
*From:* Jon Alan Wieser
*Sent:* Tuesday, December 30, 2014 8:11 PM
*To:* jorge luis
*Cc:* Kristin Elizabeth Maple
*Subject:* Re: [Freesurfer] longitudinal statistics LGI
Hi Jorge,
Following your instructions, so far we have done the following:
1-Read your label
lhcortex =
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');
3-Fit a vertex-wise lme model with two random effects for the intercept
term and time eg.:
lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);
4-Fit a vertex-wise lme model with two random effects for the intercept
term and cannabis use eg.:
lhstats2 = lme_mass_fit_vw(X, [1 3], lhY, ni, lhcortex);
lhstats3 = lme_mass_fit_vw(X, [1 2 6], lhY, ni, lhcortex);
%intercept_time_gender
lhstats4 = lme_mass_fit_vw(X, [1 2 7], lhY, ni, lhcortex);
%intercept_time_age
lhstats5 = lme_mass_fit_vw(X, [1 2 3 6 ], lhY, ni, lhcortex);
%intercept_time_cannabis_gender
We displayed the lREML data on the surface models in matlab. In some
cases,(when there were 3 or more effects ( i.e. 1 2 6) ) the lreml values
had real and imaginary values, so I displayed the ABS value of the lreml
We need to know the following:
1. How do we model this:
Intercept, time, age, gender, Alcohol, other drugs vs.
Intercept, time, age, Gender, Alcohol, Other drug, cannabis
2. Correct for multiple comparisons
3. Open these in Freesurfer, significance maps using tksurfer ( P
0.05)
Is it only visual, or is there a significance test between the two models
4. How do we get a map that demonstrates the unique effect of
cannabis
5. What Contrast matrix do we use for the LME_mass_F program
Thanks
Jon
--
*From:* jorge luis jbernal0...@yahoo.es
*Sent:* Wednesday, December 17, 2014 9:25 AM
*To:* Freesurfer support list; Jon Alan Wieser
*Cc:* Krista Lisdahl Medina; alicia.thomas@gmail.com
*Subject:* Re: [Freesurfer] longitudinal statistics LGI
Hi Jon
We recommend to order the columns of your design matrix in the
following way: First, the intercept term (which is a column of ones);
second, the time covariate; third, any time-varying covariates (eg.
cannabis use); fourth, the group covariates of interest (eg. a binary
variable indicating whether the subject is a patient or control) and their
interactions with the time-varying covariates; finally any other nuisance
time-invariant covariate (eg. gender). So your design matrix is comprised
by the following columns:
1. Intercept (a column of ones)
2. Time since baseline
3. cannabis use
[Freesurfer] freesurfer pipeline for sub mm voxel resolution
Hi All, I am working with some 7T data with 0.7 mm isotropic voxels and wanted to know if free surfer pipeline (version 5.3) can work these images ? I also have FLAIR images and wanted to know if I can use the two to create myelin maps ? Please suggest. Thanks Ri ___ 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] Longitudinal - varying geometries
Thanks, Martin. It is unfortunate to hear such news, but they are of course accurate. Hopefully this affects a small subset of subjects, and I will be able to add a covariate to it. Regards, Pedro Rosa. On Wednesday, April 1, 2015 at 12:30 PM, Martin Reuter wrote: Hi Pedro, there is really no way to fix it. Especially if all you subjects changed acquisition. If it is only a small subset, you can then include a co-variable to account for this in your stats. You should then also test whether one group has more of these cases than the other, or if it is distributed evenly (in case you run a group analysis). If you are interested in analyzing other co-variates (drug dose) you need to test if there is a correlation with acquisition, etc. Reslicing will not help at all. Adding another reslicing step to only some images will clearly bias results. If this change in acquisition has happened for most or all your subjects, you can scan a subset back-to-back (with removal from scanner), with the different protocols to see how large the effect is. The problem here is that you need to scan a decent number to trust those results. Best, Martin On 04/01/2015 11:21 AM, Pedro Rosa wrote: Hi Martin, Thank you for your answer. Is there a way to fix it? Can reslicing help? Or to try compenate for it in the processing or statistics? Regards -- Pedro Rosa On Apr 1, 2015, at 12:13, Martin Reuter mreu...@nmr.mgh.harvard.edu (mailto:mreu...@nmr.mgh.harvard.edu) wrote: Hi Pedro, yes, there was a bug (well, not really a bug but the check was oversensitive). It was testing too many image parameters, some of them could be problematic (e.g. different voxel sizes across time), and some not. Looking at your attached files, you can see that the voxel sizes differ significantly between the baseline and the follow-up Baseline: dimensions: 256 x 256 x 124 voxel sizes: 0.8594, 0.8594, 1.5000 Follow-up: dimensions: 256 x 256 x 124 voxel sizes: 1.0938, 1.0938, 1.5000 This can induce a bias. You need to keep imaging parameters fixed in a longitudinal study, else you'll not know if changes are anatomical changes or induced by the different imaging. Best, Martin On 04/01/2015 06:43 AM, Pedro Rosa - Gmail wrote: Dear FreeSurfers, I have read in the Mailing list (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html and others) other users asking questioning in regard of a Warning from FreeSurfer 5.3 longitudinal pipeline (-base step): \n*** WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ***\n I am working in a sample with a longotudinal design which receives this warn, although there was no change in hardware, and (supposedly) the acquisition protocol was the same. As requested by Martin in former posts in the Mailing List, I attached the output from mri_info */rawavg.mgz. I would like to know if these differences should be considered a bias in a longitudinal study and, if they should, if there is a way to fix it. Regards, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu (mailto:mreu...@nmr.mgh.harvard.edu) reu...@mit.edu (mailto:reu...@mit.edu) Web : http://reuter.mit.edu ___ 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
Re: [Freesurfer] Longitudinal - varying geometries
Hi Martin, Thank you for your answer. Is there a way to fix it? Can reslicing help? Or to try compenate for it in the processing or statistics? Regards -- Pedro Rosa On Apr 1, 2015, at 12:13, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Pedro, yes, there was a bug (well, not really a bug but the check was oversensitive). It was testing too many image parameters, some of them could be problematic (e.g. different voxel sizes across time), and some not. Looking at your attached files, you can see that the voxel sizes differ significantly between the baseline and the follow-up Baseline: dimensions: 256 x 256 x 124 voxel sizes: 0.8594, 0.8594, 1.5000 Follow-up: dimensions: 256 x 256 x 124 voxel sizes: 1.0938, 1.0938, 1.5000 This can induce a bias. You need to keep imaging parameters fixed in a longitudinal study, else you'll not know if changes are anatomical changes or induced by the different imaging. Best, Martin On 04/01/2015 06:43 AM, Pedro Rosa - Gmail wrote: Dear FreeSurfers, I have read in the Mailing list (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html and others) other users asking questioning in regard of a Warning from FreeSurfer 5.3 longitudinal pipeline (-base step): \n*** WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ***\n I am working in a sample with a longotudinal design which receives this warn, although there was no change in hardware, and (supposedly) the acquisition protocol was the same. As requested by Martin in former posts in the Mailing List, I attached the output from mri_info */rawavg.mgz. I would like to know if these differences should be considered a bias in a longitudinal study and, if they should, if there is a way to fix it. Regards, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer 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] -per-run analysis in native space
I can't tell from that message. Can you copy mask.nii.gz and rho1mn.nii.gz somewhere I can access? On 04/01/2015 12:14 PM, SHAHIN NASR wrote: Hi Doug, Selxavg3-sess started without any problem but then I faced the below error. Do you know what is the problem? Global In-Mask Mean = 1316.7 (8.68411) Rescale Target = 100 RescaleFactor = 0.0759477 OLS Residual Pass run 1t= 0.0 Saving rho1 run 2t=144.1 Saving rho1 run 3t=289.9 Saving rho1 run 4t=432.6 Saving rho1 run 5t=580.0 Saving rho1 run 6t=731.8 Saving rho1 run 7t=884.9 Saving rho1 run 8t=1042.3 Saving rho1 run 9t=1194.9 Saving rho1 run 10t=1341.4 Saving rho1 Smoothing ACF /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only: Segmentation fault voxelvolume 1 mm3 Loading mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz Search region is 708874 voxels = 708874.00 mm3 Smoothing input by fwhm=20.00, gstd=8.493218 Segmentation fault (core dumped) ERROR: /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n On Fri, Mar 27, 2015 at 3:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Yes. Note that that will produce huge files (float images 256^3 by number of time points). doug On 03/27/2015 01:50 PM, SHAHIN NASR wrote: Hi Surfers, I want to find a way to analyze subcortical activities in native space and still take advantage of per-run registration. As far as I understand, this is not possible in current preproc-sess. We need one extra step in which we have to map all fmcpr.nii.gz files to subject's orig.mgz. I am trying: mri_vol2vol --mov fmcpr.nii.gz --o fmcpr.native.nii.gz --fstarg orig.mgz --reg register.dof6.dat --no-save-reg --interp trilin in my mind, it is equivalent of what preproc-sess does when we use -mni305 flag (it uses mri_vol2vol to map fmcpr to mni space). Am I right? -- 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
[Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?
Dear all, having phasemaps, generated with AFNI, I would like to extract the visual areas as ROI from a surface view (infalted, flatmap or sth. like this). Steps I've tried: As I'm already familar with freeview and a bit with tksurfer I tried to use them to do that. After reading through the freesurfer-mailinglist and wiki, it seems not possible to extract ROI from surface view. Right? tksurfer can be used to extract i.e. cut, ROI but the colorkey can't be set colorwheel alike. rtview can be used to extract ROI and can have a colorwheel colorcode but expects radian values (sin, cos, and kind of significance values). I converted the phasemaps to sin and cos values. Loading these niftis shows, that the alignment in rtview is wrong. It seems some kind of rotated. The code: # coregister (gives identity matrix because it is already coregistered to anatomy) mov=sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz ref=/sub001/templates/t1w/brain.nii.gz reg=new_coreg.dat tkregister2 --s sub001 --targ $ref --mov $mov --regheader --reg $reg # alignment is wrong but colorcode looks as expected rtview --s sub001 --reg $reg --rh --polar --real sub001_pre0_Tstim32_afniPOLpfd_flirt_cos.nii.gz --imag sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz --fsig sub001_pre0_Tstim32_afniPOLpfd_flirt_sig.nii.gz # gives proper alignment # tksurfer sub001 rh inflated -overlay pre0_Tstim32_afniPOLpfd_cos.nii.gz -overlay-reg-identity freeview -v sub001/templates/t1w/brain.nii.gz sub001_pre0_Tstim32_afniPOLpfd_flirt_sin.nii.gz:reg=$reg The coregistration matrix new_coreg.dat sub001 0.699928 0.67 0.15 9.99403953552e-01 0.000e+00 1.862645149230957e-09 -1.340251287729188e-06 0.000e+00 9.99403953552e-01 0.000e+00 2.139647040166892e-05 0.000e+00 1.490116119384766e-08 1.000e+00 -2.403078542556614e-05 0 0 0 1 round Thanks, Falko ___ 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] -per-run analysis in native space
Hi Doug, Selxavg3-sess started without any problem but then I faced the below error. Do you know what is the problem? Global In-Mask Mean = 1316.7 (8.68411) Rescale Target = 100 RescaleFactor = 0.0759477 OLS Residual Pass run 1t= 0.0 Saving rho1 run 2t=144.1 Saving rho1 run 3t=289.9 Saving rho1 run 4t=432.6 Saving rho1 run 5t=580.0 Saving rho1 run 6t=731.8 Saving rho1 run 7t=884.9 Saving rho1 run 8t=1042.3 Saving rho1 run 9t=1194.9 Saving rho1 run 10t=1341.4 Saving rho1 Smoothing ACF /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only: Segmentation fault voxelvolume 1 mm3 Loading mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz Search region is 708874 voxels = 708874.00 mm3 Smoothing input by fwhm=20.00, gstd=8.493218 Segmentation fault (core dumped) ERROR: /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only -- ERROR: fast_selxavg3() failed\n On Fri, Mar 27, 2015 at 3:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Yes. Note that that will produce huge files (float images 256^3 by number of time points). doug On 03/27/2015 01:50 PM, SHAHIN NASR wrote: Hi Surfers, I want to find a way to analyze subcortical activities in native space and still take advantage of per-run registration. As far as I understand, this is not possible in current preproc-sess. We need one extra step in which we have to map all fmcpr.nii.gz files to subject's orig.mgz. I am trying: mri_vol2vol --mov fmcpr.nii.gz --o fmcpr.native.nii.gz --fstarg orig.mgz --reg register.dof6.dat --no-save-reg --interp trilin in my mind, it is equivalent of what preproc-sess does when we use -mni305 flag (it uses mri_vol2vol to map fmcpr to mni space). Am I right? -- 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/ -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Label to Nii Conversion
I have a label file on the surface, but want to be able to use it to extract surface data that is already in nifti format (dimensions: [2737 1 6]). Is there a way to convert a label to nifti? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ 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] hello freesurfer developer~
You're dicom file is jpeg compressed which FS version 5.3 does not handle. Get the two files from below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/dcmdjpeg.fs ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert Copy into $FREESURFER_HOME/bin (make a backup of mri_convert first) rehash and try again doug On 04/01/2015 01:14 PM, A-reum Min wrote: Hello My name is areum. I've got a problem while freesurfer subjects reconstruction. I have 37 subjects(control+patient) data. Number of each subject dicom file is 244. my FREESURFER_HOME is /usr/local/freesurfer my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR (K-1 image is each subjects file(contained dicom file), K-3 image is subject(no.1)'s 244 dicom file.) When i type [areum@localhost 1]# recon-all -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 (subj001 means that contain the first subjects reconstructed data) then, error occured.. Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/PISA_SPGR/subj001 mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /usr/local/freesurfer/subjects/PISA_SPGR/subj001/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm /usr/local/freesurfer/subjects/PISA_SPGR/subj001/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 Ref Series No = 3 Found 246 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.4.70-- ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) jpegUID: --1.2.840.10008.1.2.4-- Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj001 exited with ERRORS at Wed Apr 1 02:17:23 JST 2015 For more details, see the log file /usr/local/freesurfer/subjects/PISA_SPGR/subj001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting * Question 1.* Is the SUBJECTS_DIR correct path? (PISA_SPGR file contained 37 each subjects file) * Question 2.* I think that '-i' converted dicom file to mgz format. So, i type the recon-all -i /first of a collection of 244 files directory -i /second of a collection of 244 files directory -all -s subj001 ... is it right? If i type the top two images, then automatically 244 images reconstruction? I have 37 subjects files (K-1 image) * Question 3.* If i recon my each subjects data, then do I have to change the path(SUBJECTS_DIR) each time to change the subject file? ex) file number (1) is subject1's dicom, file number (2) is subject2' dicom file so, am i just finished (1)data , do i change my SUBJECTS_DIR path for recon to subjets data(2) ? ) * Question 4.* As you can see that K-6 image is subject dicom jpeg... can i use this one? or convert another format image? ___ 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.
Re: [Freesurfer] epidewarp?
Use --fsm shiftmap.nii.gz (ie, it needs an extension) On 04/01/2015 05:02 PM, Marco Loggia, PhD wrote: Hi Doug, I just noticed that when I run epidewarp, it gives me a strange 'if: Expression Syntax' error message, even if I have no if-statements in my script (see below for an example of usage). Note that I use the full path for epidewarp because I am using FSL 5.0.7. Is this a bug? Thanks, Marco dirpath=/autofs/cluster/vitaly/marco/CuffFM cd $dirpath/CuffFM_CTRL005/focus1 /usr/local/freesurfer/dev/bin/epidewarp.fsl --mag $dirpath/CuffFM_CTRL005/fieldmap/fieldmap1.nii --dph $dirpath/CuffFM_CTRL005/fieldmap/fieldmap2.nii --epi bold.nii --tediff 2.54 --esp .48 --sigma 2 --vsm shiftmap --epidw bold_dw.nii ___ 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] epidewarp?
Hi Doug, I just noticed that when I run epidewarp, it gives me a strange 'if: Expression Syntax' error message, even if I have no if-statements in my script (see below for an example of usage). Note that I use the full path for epidewarp because I am using FSL 5.0.7. Is this a bug? Thanks, Marco dirpath=/autofs/cluster/vitaly/marco/CuffFM cd $dirpath/CuffFM_CTRL005/focus1 /usr/local/freesurfer/dev/bin/epidewarp.fsl --mag $dirpath/CuffFM_CTRL005/fieldmap/fieldmap1.nii --dph $dirpath/CuffFM_CTRL005/fieldmap/fieldmap2.nii --epi bold.nii --tediff 2.54 --esp .48 --sigma 2 --vsm shiftmap --epidw bold_dw.nii ___ 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.
