[Freesurfer] Mixed anisotropic data
Dear Friends, I have used a mixed set of images from 1.5T and 3.0T scanners with anisotropic voxel size in my study. I used Freesurfer tools for converting them to isotropic voxel size before segmentation and reconvert to initial state after segmentation. It is appreciated if someone let me know using such a mixed anisotropic data causes any side effect in the volume measurement or not. I will be also thankful if you could introduce a reference that discusses the effect. Best Regards, Fari CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us. ___ 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] White matter segmentation
Dear All, I want to segment white matter into 131xx and 141xx label series. I used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone guide me how could I do this? Regards, Fari CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us. ___ 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] Analyze to nii convertor
Hi Bruce, The problem is solved by adding .img extension to input file name, but I have a new problem. The origin of the output file is not zero. Is there any switch for tuning the origin. My actual command line is: /usr/local/freesurfer/bin/mri_convert -i ./FLAIR_Sample.img -it analyze -ot nii -o FLAIR_Sample.nii Thanks, Fari From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Thursday, January 21, 2016 8:56 AM To: Freesurfer support list Subject: Re: [Freesurfer] Analyze to nii convertor Hi Fari we need the full command line and screen output in order to help you. cheers Bruce On Thu, 21 Jan 2016, Mahmoudi, Fariborz wrote: > > Dear All, > > I have a set of images with analyze 75 (img/hdr) format. I want to convert > them to .nii single file format. I used the following command: > > mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file > > But the output file has not proper nii format, When I drag the file in the > MRIcro I just see a single slice with scrambled picture. It is appreciated > if anybody could help me and let me know which switches I should use. > > Thanks, > > Fari > > > > > > > CONFIDENTIALITY NOTICE: This email contains information from the sender that > may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected > from disclosure. This email is intended for use only by the person or entity > to whom it is addressed. If you are not the intended recipient, any use, > disclosure, copying, distribution, printing, or any action taken in reliance > on the contents of this email, is strictly prohibited. If you received this > email in error, please contact the sending party by reply email, delete the > email from your computer system and shred any paper copies. > > Note to Patients: There are a number of risks you should consider before > using e-mail to communicate with us. See our Privacy & Security page on > www.henryford.com for more detailed information as well as information > concerning MyChart, our new patient portal. If you do not believe that our > policy gives you the privacy and security protection you need, do not send > e-mail or Internet communications to us. > ___ 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] Analyze to nii convertor
Dear All, I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command: mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file But the output file has not proper nii format, When I drag the file in the MRIcro I just see a single slice with scrambled picture. It is appreciated if anybody could help me and let me know which switches I should use. Thanks, Fari CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us. ___ 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] inf-lat-vent
Hi all, Who knows what is exactly meaning of inf-lat-vent? Thanks, Fari ___ 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.
