Hello Bruce,
Sorry! The first email was too big and the mailing list rejected me. My image was already in Jpeg though.
Sincerely, Ye
On Wed, Jun 26, 2013 at 5:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Ye,
can you cc the list so that others can help you? 787 would usually be too many files for an anatomical. Something on the order of 170-256 is more typical. If you visualize them the white matter should be bright, the gray matter darker and the CSF very dark
Bruce
On Wed, 26 Jun 2013, ye tian wrote:
Dear Bruce,
I just confirmed a few hours ago that I indeed have structural MRI data though. I have attached an example of the last 787 files from my data below. In fact, I tried to use only those to reconstruct my volumes and surfaces.
Do they serve as inputs to freesurfer?
Thank you very much!
Sincerely, Ye
On Wed, Jun 26, 2013 at 5:04 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: no, once they have been acquired you can't change anything. You have to hope that they also acquired structural data in addition to the functional data (which is quite common). You can't change the way your images were formed posthoc...
On Wed, 26 Jun 2013, ye tian wrote: Dear Bruce, If I understand correctly, I should bring these images back to the scanner and change some settings. Am I right? Sincerely, Ye On Wed, Jun 26, 2013 at 4:59 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: you need to know what different scan types were acquired. The ones you showed were the fMRI time-series and designed to hilight changes in blood oxygenation level, which is an indirect marker of changes in neural firing, not anatomy On Wed, 26 Jun 2013, ye tian wrote: Dear Bruce, I inherited the data from a previous graduate student. I sent out a message to learn more information about the scanner a few days ago. What information do I need to know about the scanner? Thank you so much for your time and effort! Sincerely, Ye On Wed, Jun 26, 2013 at 4:41 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Ye you can't convert it, you have to acquire it that way. Where did you get your data? Bruce On Wed, 26 Jun 2013, ye tian wrote: Dear Bruce, Sorry for my lack of knowledge. I looked online, but couldn't find how to convert MRI data to T1-weighted anatomical. Would you please shine some light on it? Thank you very much! Sincerely, Ye On Wed, Jun 26, 2013 at 4:21 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Ye you need to give recon-all a T1-weighted anatomical (e.g. mprage, SPGR/FLASH, etc...), not the fMRI data. cheers Bruce On Wed, 26 Jun 2013, ye tian wrote: Dear Bruce, Recon-all exits with the following error ERROR: input(s) cannot have multiple frames! $SUBJECTS_DIR/Barba50527_2/**mri/orig/001.mgz has 439 frames If I open 001.mgz using freeview, I obtain the image in the attachment saved as freeview 001.mgz.png. In order to make sure that my problem does not come from further upstream, I am including the major steps that I took to get to this error. MAJOR STEPS STEP0: My inherited data has names BARBA50527.MR.MEDITATE_**MEDITATION.#.#.year.month.day.**#.#.#.#.#.IMA where each # is a string of numbers.
STEP1: The images can be grouped into five categories, according to the numbers in the names that occupy the positions of the red #: 1.1-1.3, 2.1, 3.1-3.160, 4.1-4.439, 5.1-5.439 [1] Note: Images from groups 4 & 5 are very different from the images of groups 1, 2 and 3. A link to a youtube video of all the images can be seen in note[1]. STEP2: recon-all -s Barba50527_2 -i /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.4.1.2010.**07.27.10.52.51
.437500.56148038.IMA -i /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.5.1.2010.**07.27.10.52.51
.437500.56148502.IMA recon-all completes without error. [2] Note: other attempts leads to different errors. See note [2] for details. STEP3: recon-all -s Barba50527_2 -autorecon1 Exits with the error message at the beginning of the email. The number 439 seems to come from the number of files in each group. USEFUL COMMENTS http://www.mail-archive.com/**freesurfer@nmr.mgh.harvard.**edu/msg23764.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23764.html
I will do it for 001.mgz and 002.mgz and will let you know how it goes. QUESTIONS 1. Do I really need to manually parse the sequence of images? If so, how? 2. I don't really need to mri_convert my files into other formats, e.g., .dcm, do I? 3. Each file from groups 4 and 5 have multiple images. Do I need to cut them into sub-images, each with one brain? Thank you very much! Sincerely, Ye NOTES: Note [1] A video of the data can be found at http://www.youtube.com/watch?**v=W8ZFGvGvHVc&list=**UUfGdQq3j1gqPAc4z6Spmu2ghttp://www.youtube.com/watch?v=W8ZFGvGvHVc&list=UUfGdQq3j1gqPAc4z6Spmu2g
On the top left corner: the white text is: current frame number / total frame number the yellow text is: the name of the frame Note[2] recon-all -s Barba50527_2 -i /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.1.1.2010.**07.27.10.52.51
.437500.56141898.IMA Completes without error recon-all -s Barba50527_2 -autorecon1 Warning: only one run found Error: MRIsample(): source matrix has zero determinant; matrix is: EOF econ-all -s Barba50527_2 -i /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.1.1.2010.**07.27.10.52.51
.437500.56141898.IMA -i /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.2.1.2010.**07.27.10.52.51
.437500.56148502.IMA -i /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.3.1.2010.**07.27.10.52.51
.437500.56148502.IMA -i /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.4.1.2010.**07.27.10.52.51
.437500.56148038.IMA -i /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.5.1.2010.**07.27.10.52.51
.437500.56148502.IMA error.log: matrix dimensionality 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<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@nmr.mgh.harvard.edu
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ye tian