Re: [Freesurfer] Regarding_ Midbrain_misalignment
Hello Dr Greve, Will you please let me know if the above said process I did to overlay brainstorm mask on colin atlas is correct? Thanks and regards, Sam On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha wrote: > Thanks Dr Douglas for your reply. Following is the list of command I used > to generate brainstem mask. > >- I first created from average subject directory, mask of brainstem >using mri_binarize command: > > mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz > >- Then converted to mni305 space using mri_convert command: > > mri_convert mdd_brainstem.mgz mdd_brainstem.mni305.mgz --apply_transform > transforms/talairach.xfm -oc 0 0 0 --conform > >- Converted the .mgz to nii.gz with command: > > mri_convert mdd_brainstem.mni305.mgz mdd_brainstem.mni305.nii.gz > > Finally overlaid it on the mni_colin_t1hires atlas using mango. > > Thanks and regards, > > Sam > > > On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve > wrote: > >> how was it created? >> >> On 6/20/17 9:41 AM, Dr Sampada Sinha wrote: >> >> Dear freesurfer experts, >> >> I am trying to over brainstem mask of my patients' group on >> mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or >> amygdala mask, but somehow the midbrain mask is shifted from the actual >> place (please see attachment). Can you please let me know how do I correct >> this error? >> >> Thanks for all your help. >> >> Kind regards, >> >> Sam >> >> -- >> Dr Sampada Sinha >> Research medical scientist (B) >> Department of Geriatric Mental Health (DGMH) >> King George Medical University >> Lucknow-226003 >> , Uttar Pradesh >> India >> >> >> >> >> >> >> >> >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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. >> >> > > > -- > Dr Sampada Sinha > Research medical scientist (B) > Department of Geriatric Mental Health (DGMH) > King George Medical University > Lucknow-226003 > , Uttar Pradesh > India > > > > > > > > > -- Dr Sampada Sinha Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India ___ 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] Regarding_ Midbrain_misalignment
Hi Sampada it's the eve of HBM and a lot of people are traveling or preparing to travel, so our response time may be longer! As for your problem, you might try mri_vol2vol instead of mri_convert. If you run it with --help and search for 'talairach' you will find a lot of useful stuff, including this example: mri_vol2vol --help . . . 3. Apply an MNI transform to data by resampling the anatomical orig.mgz into talairach space using bert/mri/transforms/talairach.xfm: First, check that the talairach.xfm is correct (this is basically the same thing as 'tkregister2 --s bert --fstal' in Example 2: cd bert/mri tkregister2 --targ orig.mgz \ --mov $FREESURFER_HOME/average/mni305.cor.mgz \ --xfm transforms/talairach.xfm --reg /tmp/reg Now resample mri_vol2vol --mov orig.mgz \ --targ $FREESURFER_HOME/average/mni305.cor.mgz \ --xfm transforms/talairach.xfm \ --o orig-in-mni305.mgz Now test the resampling: tkregister2 --mov orig-in-mni305.mgz \ --targ $FREESURFER_HOME/average/mni305.cor.mgz \ --reg /tmp/reg --regheader note that you can just specify the output file as mdd_brainstem.mni305.nii.gz and it will be saved in nifti. No need for an additional step cheers Bruce On Sun, 25 Jun 2017, Dr Sampada Sinha wrote: Hello Dr Greve, Will you please let me know if the above said process I did to overlay brainstorm mask on colin atlas is correct? Thanks and regards, Sam On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha wrote: Thanks Dr Douglas for your reply. Following is the list of command I used to generate brainstem mask. * I first created from average subject directory, mask of brainstem using mri_binarize command: mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz * Then converted to mni305 space using mri_convert command: mri_convert mdd_brainstem.mgz mdd_brainstem.mni305.mgz --apply_transform transforms/talairach.xfm -oc 0 0 0 --conform * Converted the .mgz to nii.gz with command: mri_convert mdd_brainstem.mni305.mgz mdd_brainstem.mni305.nii.gz Finally overlaid it on the mni_colin_t1hires atlas using mango. Thanks and regards, Sam On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve wrote: how was it created? On 6/20/17 9:41 AM, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to over brainstem mask of my patients' group on mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or amygdala mask, but somehow the midbrain mask is shifted from the actual place (please see attachment). Can you please let me know how do I correct this error? Thanks for all your help. Kind regards, Sam -- Dr Sampada Sinha Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India ___ 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. -- Dr Sampada Sinha Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003, Uttar Pradesh India -- Dr Sampada Sinha Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003, Uttar Pradesh India ___ 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] Regarding_ Midbrain_misalignment
Thanks Dr Fischl, I will surely try that. Appreciate all your help at the busy time of this year! Thanks and regards, Sam On Sun, Jun 25, 2017 at 8:12 PM, Bruce Fischl wrote: > Hi Sampada > > it's the eve of HBM and a lot of people are traveling or preparing to > travel, so our response time may be longer! > > As for your problem, you might try mri_vol2vol instead of mri_convert. If > you run it with --help and search for 'talairach' you will find a lot of > useful stuff, including this example: > > mri_vol2vol --help > . > . > . > 3. Apply an MNI transform to data by resampling the anatomical orig.mgz > into talairach space using bert/mri/transforms/talairach.xfm: > > First, check that the talairach.xfm is correct (this is basically the same > thing as 'tkregister2 --s bert --fstal' in Example 2: > > cd bert/mri > tkregister2 --targ orig.mgz \ > --mov $FREESURFER_HOME/average/mni305.cor.mgz \ > --xfm transforms/talairach.xfm --reg /tmp/reg > > Now resample > mri_vol2vol --mov orig.mgz \ > --targ $FREESURFER_HOME/average/mni305.cor.mgz \ > --xfm transforms/talairach.xfm \ > --o orig-in-mni305.mgz > > Now test the resampling: > tkregister2 --mov orig-in-mni305.mgz \ > --targ $FREESURFER_HOME/average/mni305.cor.mgz \ > --reg /tmp/reg --regheader > > > > note that you can just specify the output file as > mdd_brainstem.mni305.nii.gz and it will be saved in nifti. No need for an > additional step > > cheers > Bruce > > > > > On Sun, 25 Jun 2017, Dr Sampada Sinha wrote: > > Hello Dr Greve, >> >> Will you please let me know if the above said process I did to overlay >> brainstorm mask on colin atlas is correct? >> >> Thanks and regards, >> >> Sam >> >> >> >> On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha < >> drsampadasi...@gmail.com> wrote: >> Thanks Dr Douglas for your reply. Following is the list of command >> I used to generate brainstem mask. >> * I first created from average subject directory, mask of brainstem >> using mri_binarize command: >> mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz >> * Then converted to mni305 space using mri_convert command: >> mri_convert mdd_brainstem.mgz mdd_brainstem.mni305.mgz --apply_transform >> transforms/talairach.xfm -oc 0 0 0 --conform >> * Converted the .mgz to nii.gz with command: >> >> mri_convert mdd_brainstem.mni305.mgz mdd_brainstem.mni305.nii.gz >> >> Finally overlaid it on the mni_colin_t1hires atlas using mango. >> >> Thanks and regards, >> >> Sam >> >> >> On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve >> wrote: >> >> how was it created? >> >> >> On 6/20/17 9:41 AM, Dr Sampada Sinha wrote: >> Dear freesurfer experts, >> >> I am trying to over brainstem mask of my patients' group on >> mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or >> amygdala mask, but somehow >> the midbrain mask is shifted from the actual place (please see >> attachment). Can you please let me know how do I correct this error? >> >> Thanks for all your help. >> >> Kind regards, >> >> Sam >> >> -- >> Dr Sampada Sinha >> Research medical scientist (B) >> Department of Geriatric Mental Health (DGMH) >> King George Medical University >> Lucknow-226003 , Uttar Pradesh >> India >> >> >> >> >> >> >> >> >> >> >> ___ >> 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. >> >> >> >> >> -- >> Dr Sampada Sinha >> Research medical scientist (B) >> Department of Geriatric Mental Health (DGMH) >> King George Medical University >> Lucknow-226003, Uttar Pradesh >> India >> >> >> >> >> >> >> >> >> >> >> >> -- >> Dr Sampada Sinha >> Research medical scientist (B) >> Department of Geriatric Mental Health (DGMH) >> King George Medical University >> Lucknow-226003, Uttar Pradesh >> India >> >> >> >> >> >> >> >> >> >> > ___ > 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.
[Freesurfer] freesurfer@nmr.mgh.harvard.edu
Hi, I am preprocessing my fMRI data acquired with Philips. when I using the command 'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .' The error occurred likes below: Found 31 total files. Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201 Subject xxx Date xxx Time 110223 Institution x. 0 Survey unknown unknown unknown unknown unknown unknown ./PS_0002 101 Survey unknown unknown unknown unknown unknown 140 ./XX_0003 301 T1W_3D_TFE_ref unknown unknown unknown unknown unknown 190 ./IM_0004 401 FE_EPI unknown unknown unknown unknown unknown 2835 ./XX_0007 501 FE_EPI_EX1 unknown unknown unknown unknown unknown 2835 ./IM_0008 601 FE_EPI_EX2 unknown unknown unknown unknown unknown 2835 ./IM_0011 701 FE_EPI_EX3 unknown unknown unknown unknown unknown 2835 ./IM_0013 801 FE_EPI_EX4 unknown unknown unknown unknown unknown 2835 ./XX_0016 901 FE_EPI_EX5 unknown unknown unknown unknown unknown 2835 ./XX_0018 1001 FE_EPI_EX6 unknown unknown unknown unknown unknown 2835 ./IM_0019 1101 FE_EPI_EX7 unknown unknown unknown unknown unknown 2835 ./XX_0022 1201 FE_EPI_EX8 unknown unknown unknown unknown unknown 2835 ./XX_0024 mri_convert ./XX_0003 ./bold/101/f.nii --nskip 0 --ndrop 0 nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./XX_0003... Starting DICOMRead2() dcmfile = ./XX_0003 dcmdir = . WARNING: tag image orientation not found in ./XX_0003 Ref Series No = 101 ERROR: bits = 0 not supported. My os is Linux 16.04 and the Freesurfer's version is 5.3. ___ 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.