[Freesurfer] skip subjects already processed
External Email - Use Caution Hello, I have a subset of subjects that were processed with an older version of FreeSurfer and would like to run FreeSurfer in the subjects directory such that it skips all the subjects already processed by my version of freesurfer and only reruns recon-all ... for those aforementioned subjects. When I do this, will the file structure and files for the subject be overwritten? How does FreeSurfer behave in this case? How does it behave for subjects directories that have already been successfully processed with the same command (including options) attempting to process it at the moment? Would appreciate any help thanks. Best, Akshay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Difference b/w White matter hyper-intensities and hypo-intensities
Hi All, There is a label named White-matter hypo-intensities (77), is it the same as white matter hyper-intensity? If not, can anyone tell me the difference? Thanks in advance, Akshay ___ 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] repeat: trouble loading nifti files
Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ===== The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Is there something wrong I am doing? How do I conform these files to 256^3mm? Any help will be greatly appreciated. Best, Akshay ___ 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] Fwd: Re: repeat: trouble loading nifti files
mri_convert path-to-nifti file mask.mgz --resample_type nearest -cs 256 On 5/7/13 2:55 PM, Bruce Fischl wrote: can you send me the full mri_convert command line that is run? On Tue, 7 May 2013, Akshay wrote: Hi Bruce Please find the file attached Best, Akshay On 5/7/13 2:40 PM, Bruce Fischl wrote: Hi Akshay is you send us that file we'll take a look. cheers Bruce On Tue, 7 May 2013, Akshay wrote: Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ===== The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Is there something wrong I am doing? How do I conform these files to 256^3mm? Any help will be greatly appreciated. Best, Akshay ___ 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
[Freesurfer] Trouble loading nifti file
Hello all, I have a problem conforming certain nifti files, the following is the log when i try to convert them, reading from /home/akshay/ADNI/137_S_1041/MIDAS_Whole_Brain_Mask/2006-11-09_09_35_11.0/S22310/ADNI_137_S_1041_MR_MIDAS_Whole_Brain_Mask_Br_20120723235935683_S22310_I317755.nii... INFO: using NIfTI-1 qform TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -4.99113e-10, -1) j_ras = (-4.99113e-10, -1, 4.99113e-10) k_ras = (-1, 4.99113e-10, 0) WARNING ===== The physical sizes are (281.25 mm, 280.14 mm, 216.72 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 282 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ===== Original Data has (1.09862, 1.09429, 1.20399) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 282 voxels for all directions Reslicing using nearest This is understood, however I want them to be conformed to 256^3 mm. If I use -cs 256 flag, it does resample the image to 256^3mm but the image is blank. Any help will be greatly appreciated. Best, Akshay ___ 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] Whole Brain definition
Hello Freesurfer experts, I am currently doing some TBM analysis and to compute whole brain atrophy I consider all the structures except ventricles and CSF from aseg.mgz in my definition. Should I also include the cortex definition from aparc+aseg? If yes, should I then use aparc+aseg or aparc.a2009s+aseg segmentation file? Any help will be greatly appreciated. Akshay Univ. of Copenhagen ___ 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] Definition of medial temporal lobe
Hello freesurfer experts, I am doing some TBM analysis and I am looking for the definition of Medial temporal lobe. According to the definitions I found out they are hippocampus+amygdala+brainstem+parahippocampal regions+entorhinal region. I can get hippocampus and amygdala ROI from aseg.mgz; however for parahippocampal and entorhinal regions should i use aparc+aseg.mgz and aparc.a2009s+aseg.mgz? Any help will be appreciated. Best, Akshay ___ 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] Definition of temporal lobe
Hello all, Which labels reside in temporal lobe? Do I look at aseg or aseg+aparc.? I am very new to freesurfer therefore forgive me for my naive questions. Best, Akshay ___ 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] Definition of anatomical regions
Hi, I have been working on a DBM based method to obtain longitudinal atrophy on some brain data. To quantify ROI, i use aseg.mgz. Several papers talk about Whole Brain, ventricular atrophy but do not actually define what substructures they use? It will be great if somebody can help me get the actual definition of whole brain and ventricles. For ex: WM Hypointensities are part of whole brain?, Since they increase in volume. Thank you , Akshay University of Copehagen ___ 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.
